diff --git a/doc/Eqs/pair_mgpt.jpg b/doc/Eqs/pair_mgpt.jpg
new file mode 100644
index 000000000..2bede7f90
Binary files /dev/null and b/doc/Eqs/pair_mgpt.jpg differ
diff --git a/doc/Eqs/pair_mgpt.tex b/doc/Eqs/pair_mgpt.tex
new file mode 100644
index 000000000..9c314df91
--- /dev/null
+++ b/doc/Eqs/pair_mgpt.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
+ + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
+ + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
+ + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )
+$$
+
+\end{document}
diff --git a/doc/Eqs/pair_smtbq1.jpg b/doc/Eqs/pair_smtbq1.jpg
new file mode 100644
index 000000000..6bfb07b77
Binary files /dev/null and b/doc/Eqs/pair_smtbq1.jpg differ
diff --git a/doc/Eqs/pair_smtbq1.tex b/doc/Eqs/pair_smtbq1.tex
new file mode 100755
index 000000000..21ae0e9a4
--- /dev/null
+++ b/doc/Eqs/pair_smtbq1.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{tot} & = & E_{ES} + E_{OO} + E_{MO} \\
+E_{ES} & = & \sum_i{\Big[ \chi_{i}^{0}Q_i + \frac{1}{2}J_{i}^{0}Q_{i}^{2} +
+ \frac{1}{2} \sum_{j\neq i}{ J_{ij}(r_{ij})f_{cut}^{R_{coul}}(r_{ij})Q_i Q_j } \Big] } \\
+E_{OO} & = & \sum_{i,j}^{i,j = O}{\Bigg[Cexp( -\frac{r_{ij}}{\rho} ) - Df_{cut}^{r_1^{OO}r_2^{OO}}(r_{ij}) exp(Br_{ij})\Bigg]} \\
+E_{MO} & = & \sum_i{E_{cov}^{i} + \sum_{j\neq i}{ Af_{cut}^{r_{c1}r_{c2}}(r_{ij})exp\Big[-p(\frac{r_{ij}}{r_0} -1) \Big] } } \\
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/Eqs/pair_smtbq2.jpg b/doc/Eqs/pair_smtbq2.jpg
new file mode 100644
index 000000000..0e2024878
Binary files /dev/null and b/doc/Eqs/pair_smtbq2.jpg differ
diff --git a/doc/Eqs/pair_smtbq2.tex b/doc/Eqs/pair_smtbq2.tex
new file mode 100755
index 000000000..8524c2586
--- /dev/null
+++ b/doc/Eqs/pair_smtbq2.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{cov}^{i(i=M,O)} & = & - \Bigg\{\eta_i(\mu \xi^{0})^2 f_{cut}^{r_{c1}r_{c2}}(r_{ij})
+\Bigg( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \Bigg)
+\delta Q_i \Big( 2\frac{n_0}{\eta_i} - \delta Q_i \Big) \Bigg\}^{1/2} \\
+\delta Q_i & = & | Q_i^{F} | - | Q_i |
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/Eqs/pair_smtbq3.jpg b/doc/Eqs/pair_smtbq3.jpg
new file mode 100644
index 000000000..1d6045916
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diff --git a/doc/Eqs/pair_smtbq3.tex b/doc/Eqs/pair_smtbq3.tex
new file mode 100755
index 000000000..5bc6e465d
--- /dev/null
+++ b/doc/Eqs/pair_smtbq3.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\xi^0 & = & \frac{\xi_O}{m} = \frac{\xi_C}{n} \\
+\frac{\beta_O}{\sqrt{m}} & = & \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}\\
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/Manual.html b/doc/Manual.html
index 527d6255e..7173f0598 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -1,472 +1,492 @@
+<HTML>
+<!-- HTML_ONLY -->
+<HEAD>
+<TITLE>LAMMPS Users Manual</TITLE>
+<META NAME="docnumber" CONTENT="24 Oct 2015 version">
+<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
+<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
+</HEAD>
+<BODY>
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-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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-
- <H1></H1><div class="section" id="lammps-documentation">
-<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="aug-2015-version">
-<h2>10 Aug 2015 version<a class="headerlink" href="#aug-2015-version" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="version-info">
-<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
-<p>The LAMMPS “version” is the date when it was released, such as 1 May
+<!-- END_HTML_ONLY -->
+
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H1></H1>
+
+<CENTER><H3>LAMMPS Documentation
+</H3></CENTER>
+<CENTER><H4>24 Oct 2015 version
+</H4></CENTER>
+<H4>Version info:
+</H4>
+<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
+feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
+the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<P>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
</P>
-
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
-LAMMPS.</li>
-</ul>
-<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.</p>
-<p>LAMMPS is a classical molecular dynamics simulation code designed to
+LAMMPS.
+</UL>
+<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator.
+</P>
+<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).</p>
-<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
+under the terms of the GNU Public License (GPL).
+</P>
+<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
-<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
-uses.</p>
-<hr class="docutils" />
-<p>The LAMMPS documentation is organized into the following sections. If
+sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
+http://lammps.sandia.gov has more information about the code and its
+uses.
+</P>
+
+
+
+
+<HR>
+
+<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.</p>
-<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.</p>
-<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
-<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What’s in the LAMMPS distribution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.26. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.27. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.28. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.29. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.30. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.31. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.32. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.33. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.34. USER-SPH package</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error & warning messages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
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+we can improve the LAMMPS documentation.
+</P>
+<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
+page</A> at Section_commands.html#comm since
+it gives quick access to documentation for all LAMMPS commands.
+</P>
+<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
+<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
+</P>
+<P><!-- RST
+</P>
+<P>.. toctree::
+ :maxdepth: 2
+ :numbered: // comment
+</P>
+<P> Section_intro
+ Section_start
+ Section_commands
+ Section_packages
+ Section_accelerate
+ Section_howto
+ Section_example
+ Section_perf
+ Section_tools
+ Section_modify
+ Section_python
+ Section_errors
+ Section_history
+</P>
+<P>Indices and tables
+==================
+</P>
+<P>* :ref:`genindex` // comment
+* :ref:`search` // comment
+</P>
+<P>END_RST -->
+</P>
+<OL><LI><!-- HTML_ONLY -->
+<A HREF = "Section_intro.html">Introduction</A>
+
+<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
+<BR>
+ 1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
+<BR>
+ 1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
+<BR>
+ 1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
+<BR>
+ 1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
+<BR></UL>
+<LI><A HREF = "Section_start.html">Getting started</A>
+
+<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
+<BR>
+ 2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
+<BR>
+ 2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
+<BR>
+ 2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
+<BR>
+ 2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
+<BR>
+ 2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
+<BR>
+ 2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
+<BR>
+ 2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
+<BR>
+ 2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
+<BR></UL>
+<LI><A HREF = "Section_commands.html">Commands</A>
+
+<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
+<BR>
+ 3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
+<BR>
+ 3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
+<BR>
+ 3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
+<BR>
+ 3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
+<BR></UL>
+<LI><A HREF = "Section_packages.html">Packages</A>
+
+<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
+<BR>
+ 4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
+<BR></UL>
+<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
+
+<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
+<BR>
+ 5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
+<BR>
+ 5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
+<BR>
+<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
+<BR>
+ 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
+<BR>
+ 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
+<BR>
+ 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
+<BR>
+ 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
+<BR>
+ 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
+<BR></UL>
+ 5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
+<BR></UL>
+<LI><A HREF = "Section_howto.html">How-to discussions</A>
+
+<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
+<BR>
+ 6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
+<BR>
+ 6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
+<BR>
+ 6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
+<BR>
+ 6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
+<BR>
+ 6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
+<BR>
+ 6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
+<BR>
+ 6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
+<BR>
+ 6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
+<BR>
+ 6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
+<BR>
+ 6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
+<BR>
+ 6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
+<BR>
+ 6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
+<BR>
+ 6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
+<BR>
+ 6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
+<BR>
+ 6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
+<BR>
+ 6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
+<BR>
+ 6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
+<BR>
+ 6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
+<BR>
+ 6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
+<BR>
+ 6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
+<BR>
+ 6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
+<BR>
+ 6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
+<BR>
+ 6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
+<BR>
+ 6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
+<BR>
+ 6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
+<BR>
+ 6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
+<BR></UL>
+<LI><A HREF = "Section_example.html">Example problems</A>
+
+<LI><A HREF = "Section_perf.html">Performance & scalability</A>
+
+<LI><A HREF = "Section_tools.html">Additional tools</A>
+
+<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
+
+<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
+<BR>
+ 10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
+<BR>
+ 10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
+<BR>
+ 10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
+<BR>
+ 10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
+<BR>
+ 10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
+<BR>
+ 10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
+<BR>
+ 10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
+<BR>
+ 10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
+<BR>
+ 10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
+<BR>
+ 10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
+<BR>
+ 10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
+<BR>
+ 10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
+<BR>
+ 10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
+<BR>
+ 10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
+<BR></UL>
+<LI><A HREF = "Section_python.html">Python interface</A>
+
+<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
+<BR>
+ 11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
+<BR>
+ 11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
+<BR>
+ 11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
+<BR>
+ 11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
+<BR>
+ 11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
+<BR>
+ 11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
+<BR>
+ 11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
+<BR></UL>
+<LI><A HREF = "Section_errors.html">Errors</A>
+
+<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
+<BR>
+ 12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
+<BR>
+ 12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
+<BR></UL>
+<LI><A HREF = "Section_history.html">Future and history</A>
+
+<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
+<BR>
+ 13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
+<BR></UL>
+
+</OL>
+
+
+
+
+
+
+
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+</HTML>
diff --git a/doc/Manual.html.html b/doc/Manual.html.html
index f76689504..0ddcdedea 100644
--- a/doc/Manual.html.html
+++ b/doc/Manual.html.html
@@ -1,318 +1,318 @@
<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Oct 2015 version">
+<META NAME="docnumber" CONTENT="23 Oct 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<!-- END_HTML_ONLY -->
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
-<CENTER><H4>22 Oct 2015 version
+<CENTER><H4>23 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
</P>
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
</HTML>
diff --git a/doc/Manual.txt b/doc/Manual.txt
index 429e86719..bf7d35a55 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,319 +1,319 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Oct 2015 version">
+<META NAME="docnumber" CONTENT="24 Oct 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<!-- END_HTML_ONLY -->
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
-5 Oct 2015 version :c,h4
+24 Oct 2015 version :c,h4
Version info: :h4
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on "this page of
the WWW site"_bug. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of upstream LAMMPS, but may be
missing some new features in LAMMPS-ICMS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have, however, not all new features in
LAMMPS-ICMS are documented immediately. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at
http://lammps.sandia.gov has more information about the code and its
uses.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
:line
The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Section_commands.html#comm at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://freecode.com/projects/htmldoc
<!-- RST
.. toctree::
:maxdepth: 2
- :numbered:
+ :numbered: // comment
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`
+* :ref:`genindex` // comment
+* :ref:`search` // comment
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)
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:link(cmd_2,Section_commands.html#cmd_2)
:link(cmd_3,Section_commands.html#cmd_3)
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: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)
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:link(howto_1,Section_howto.html#howto_1)
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:link(howto_13,Section_howto.html#howto_13)
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: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)
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: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)
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">3.7. Compute styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#improper-style-potentials">3.12. Improper_style potentials</a></li>
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<div class="section" id="commands">
<h1>3. Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h1>
<p>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.</p>
<div class="line-block">
<div class="line">3.1 <a class="reference internal" href="#cmd-1"><span>LAMMPS input script</span></a></div>
<div class="line">3.2 <a class="reference internal" href="#cmd-2"><span>Parsing rules</span></a></div>
<div class="line">3.3 <a class="reference internal" href="#cmd-3"><span>Input script structure</span></a></div>
<div class="line">3.4 <a class="reference internal" href="#cmd-4"><span>Commands listed by category</span></a></div>
<div class="line">3.5 <a class="reference internal" href="#cmd-5"><span>Commands listed alphabetically</span></a></div>
<div class="line"><br /></div>
</div>
<div class="section" id="lammps-input-script">
<span id="cmd-1"></span><h2>3.1. LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline">¶</a></h2>
<p>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.</p>
<p>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:</p>
<p>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:</p>
<div class="highlight-python"><div class="highlight"><pre>timestep 0.5
run 100
run 100
</pre></div>
</div>
<p>does something different than this sequence:</p>
<div class="highlight-python"><div class="highlight"><pre>run 100
timestep 0.5
run 100
</pre></div>
</div>
<p>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.</p>
<p>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.</p>
<p>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <a class="reference internal" href="processors.html"><em>processors</em></a> and
<a class="reference internal" href="boundary.html"><em>boundary</em></a> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.</p>
<p>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <a class="reference internal" href="Section_errors.html"><em>This section</em></a> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.</p>
<hr class="docutils" />
</div>
<div class="section" id="parsing-rules">
<span id="cmd-2"></span><h2>3.2. Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h2>
<p>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.</p>
<p>Here is how each line in the input script is parsed by LAMMPS:</p>
<p>(1) If the last printable character on the line is a “&” character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the “&” character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using “&” characters.</p>
<p>(2) All characters from the first “#” character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing “&” character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading “#” will comment out the entire command.</p>
<p>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).</p>
<p>If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names “myTemp” and
“x”.</p>
<p>How the variable is converted to a text string depends on what style
of variable it is; see the <a class="reference external" href="variable">variable</a> doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple “words” (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.</p>
<p>As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an “immediate” variable and
evaluated as an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:</p>
<div class="highlight-python"><div class="highlight"><pre>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</pre></div>
</div>
<p>can be replaced by</p>
<div class="highlight-python"><div class="highlight"><pre>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</pre></div>
</div>
<p>so that you do not have to define (or discard) a temporary variable X.</p>
<p>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:</p>
<div class="highlight-python"><div class="highlight"><pre>variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
</pre></div>
</div>
<p>Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a>.</p>
<p>See the <a class="reference internal" href="variable.html"><em>variable</em></a> command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.</p>
<p>(4) The line is broken into “words” separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.</p>
<p>(5) The first word is the command name. All successive words in the
line are arguments.</p>
<p>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the “&” character is used, as described above. When
the lines are concatenated together (and the “&” characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case “&” characters are not
needed. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
</pre></div>
</div>
<p>In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.</p>
<p>See the <a class="reference internal" href="dump_modify.html"><em>dump modify format</em></a>, <a class="reference internal" href="print.html"><em>print</em></a>,
<a class="reference internal" href="if.html"><em>if</em></a>, and <a class="reference internal" href="python.html"><em>python</em></a> commands for examples.</p>
<p>A “#” or “$” character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If the argument is itself a command that requires a
quoted argument (e.g. using a <a class="reference internal" href="print.html"><em>print</em></a> command as part of an
<a class="reference internal" href="if.html"><em>if</em></a> or <a class="reference internal" href="run.html"><em>run every</em></a> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="input-script-structure">
<span id="cmd-3"></span><h2>3.3. Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline">¶</a></h2>
<p>This section describes the structure of a typical LAMMPS input script.
The “examples” directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<a class="reference internal" href="Section_example.html"><em>Section_example</em></a>, and animated on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
<p>A LAMMPS input script typically has 4 parts:</p>
<ol class="arabic simple">
<li>Initialization</li>
<li>Atom definition</li>
<li>Settings</li>
<li>Run a simulation</li>
</ol>
<p>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.</p>
<ol class="arabic simple">
<li>Initialization</li>
</ol>
<p>Set parameters that need to be defined before atoms are created or
read-in from a file.</p>
<p>The relevant commands are <a class="reference internal" href="units.html"><em>units</em></a>,
<a class="reference internal" href="dimension.html"><em>dimension</em></a>, <a class="reference internal" href="newton.html"><em>newton</em></a>,
<a class="reference internal" href="processors.html"><em>processors</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</em></a>,
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a>, <a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a>.</p>
<p>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>,
<a class="reference internal" href="angle_style.html"><em>angle_style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper_style</em></a>.</p>
<ol class="arabic simple" start="2">
<li>Atom definition</li>
</ol>
<p>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
<a class="reference internal" href="region.html"><em>region</em></a>, <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>. The entire set of atoms can be
duplicated to make a larger simulation using the
<a class="reference internal" href="replicate.html"><em>replicate</em></a> command.</p>
<ol class="arabic simple" start="3">
<li>Settings</li>
</ol>
<p>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.</p>
<p>Force field coefficients are set by these commands (they can also be
set in the read-in files): <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>,
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>,
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a>,
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>, <a class="reference internal" href="dielectric.html"><em>dielectric</em></a>,
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>.</p>
<p>Various simulation parameters are set by these commands:
<a class="reference internal" href="neighbor.html"><em>neighbor</em></a>, <a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>,
<a class="reference internal" href="group.html"><em>group</em></a>, <a class="reference internal" href="timestep.html"><em>timestep</em></a>,
<a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>,
<a class="reference internal" href="min_style.html"><em>min_style</em></a>, <a class="reference internal" href="min_modify.html"><em>min_modify</em></a>.</p>
<p>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <a class="reference internal" href="fix.html"><em>fix</em></a> command comes in many flavors.</p>
<p>Various computations can be specified for execution during a
simulation using the <a class="reference internal" href="compute.html"><em>compute</em></a>,
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>, and <a class="reference internal" href="variable.html"><em>variable</em></a>
commands.</p>
<p>Output options are set by the <a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="dump.html"><em>dump</em></a>,
and <a class="reference internal" href="restart.html"><em>restart</em></a> commands.</p>
<ol class="arabic simple" start="4">
<li>Run a simulation</li>
</ol>
<p>A molecular dynamics simulation is run using the <a class="reference internal" href="run.html"><em>run</em></a>
command. Energy minimization (molecular statics) is performed using
the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command. A parallel tempering
(replica-exchange) simulation can be run using the
<a class="reference internal" href="temper.html"><em>temper</em></a> command.</p>
<hr class="docutils" />
</div>
<div class="section" id="commands-listed-by-category">
<span id="cmd-4"></span><h2>3.4. Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline">¶</a></h2>
<p>This section lists all LAMMPS commands, grouped by category. The
<a class="reference internal" href="#cmd-5"><span>next section</span></a> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command’s documentation.</p>
<p>Initialization:</p>
<p><a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a>, <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>,
<a class="reference internal" href="boundary.html"><em>boundary</em></a>, <a class="reference internal" href="dimension.html"><em>dimension</em></a>,
<a class="reference internal" href="newton.html"><em>newton</em></a>, <a class="reference internal" href="processors.html"><em>processors</em></a>, <a class="reference internal" href="units.html"><em>units</em></a></p>
<p>Atom definition:</p>
<p><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
<a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="read_dump.html"><em>read_dump</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>,
<a class="reference internal" href="region.html"><em>region</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a></p>
<p>Force fields:</p>
<p><a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>, <a class="reference internal" href="angle_style.html"><em>angle_style</em></a>,
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>,
<a class="reference internal" href="dielectric.html"><em>dielectric</em></a>, <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>,
<a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a>,
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper_style</em></a>,
<a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>,
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>,
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a>,
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></p>
<p>Settings:</p>
<p><a class="reference internal" href="comm_style.html"><em>comm_style</em></a>, <a class="reference internal" href="group.html"><em>group</em></a>, <a class="reference internal" href="mass.html"><em>mass</em></a>,
<a class="reference internal" href="min_modify.html"><em>min_modify</em></a>, <a class="reference internal" href="min_style.html"><em>min_style</em></a>,
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>,
<a class="reference internal" href="set.html"><em>set</em></a>, <a class="reference internal" href="timestep.html"><em>timestep</em></a>, <a class="reference internal" href="velocity.html"><em>velocity</em></a></p>
<p>Fixes:</p>
<p><a class="reference internal" href="fix.html"><em>fix</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <a class="reference internal" href="unfix.html"><em>unfix</em></a></p>
<p>Computes:</p>
<p><a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>,
<a class="reference internal" href="uncompute.html"><em>uncompute</em></a></p>
<p>Output:</p>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="dump_image.html"><em>dump movie</em></a>,
<a class="reference internal" href="restart.html"><em>restart</em></a>, <a class="reference internal" href="thermo.html"><em>thermo</em></a>,
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a>, <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>,
<a class="reference internal" href="undump.html"><em>undump</em></a>, <a class="reference internal" href="write_data.html"><em>write_data</em></a>,
<a class="reference internal" href="write_dump.html"><em>write_dump</em></a>, <a class="reference internal" href="write_restart.html"><em>write_restart</em></a></p>
<p>Actions:</p>
<p><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>,
<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="change_box.html"><em>change_box</em></a>,
<a class="reference internal" href="minimize.html"><em>minimize</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a> <a class="reference internal" href="prd.html"><em>prd</em></a>,
<a class="reference internal" href="rerun.html"><em>rerun</em></a>, <a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="temper.html"><em>temper</em></a></p>
<p>Miscellaneous:</p>
<p><a class="reference internal" href="clear.html"><em>clear</em></a>, <a class="reference internal" href="echo.html"><em>echo</em></a>, <a class="reference internal" href="if.html"><em>if</em></a>,
<a class="reference internal" href="include.html"><em>include</em></a>, <a class="reference internal" href="jump.html"><em>jump</em></a>, <a class="reference internal" href="label.html"><em>label</em></a>,
<a class="reference internal" href="log.html"><em>log</em></a>, <a class="reference internal" href="next.html"><em>next</em></a>, <a class="reference internal" href="print.html"><em>print</em></a>,
<a class="reference internal" href="shell.html"><em>shell</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
<hr class="docutils" />
</div>
<div class="section" id="individual-commands">
<span id="comm"></span><span id="cmd-5"></span><h2>3.5. Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline">¶</a></h2>
<p>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <a class="reference internal" href="#cmd-4"><span>previous section</span></a> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command’s documentation.</p>
<table border="1" class="docutils">
<colgroup>
<col width="17%" />
<col width="15%" />
<col width="17%" />
<col width="17%" />
<col width="17%" />
<col width="17%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></td>
<td><a class="reference internal" href="angle_style.html"><em>angle_style</em></a></td>
<td><a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a></td>
<td><a class="reference internal" href="atom_style.html"><em>atom_style</em></a></td>
<td><a class="reference internal" href="balance.html"><em>balance</em></a></td>
<td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="bond_style.html"><em>bond_style</em></a></td>
<td><a class="reference internal" href="boundary.html"><em>boundary</em></a></td>
<td><a class="reference internal" href="box.html"><em>box</em></a></td>
<td><a class="reference internal" href="change_box.html"><em>change_box</em></a></td>
<td><a class="reference internal" href="clear.html"><em>clear</em></a></td>
<td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
<td><a class="reference internal" href="compute.html"><em>compute</em></a></td>
<td><a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a></td>
<td><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></td>
<td><a class="reference internal" href="create_bonds.html"><em>create_bonds</em></a></td>
<td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
<td><a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></td>
<td><a class="reference internal" href="dielectric.html"><em>dielectric</em></a></td>
<td><a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a></td>
<td><a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a></td>
<td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
<td><a class="reference internal" href="dump_image.html"><em>dump image</em></a></td>
<td><a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a></td>
<td><a class="reference internal" href="dump_image.html"><em>dump movie</em></a></td>
<td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
<td><a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></td>
<td><a class="reference internal" href="group.html"><em>group</em></a></td>
<td><a class="reference internal" href="if.html"><em>if</em></a></td>
<td><a class="reference internal" href="info.html"><em>info</em></a></td>
<td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
<td><a class="reference internal" href="include.html"><em>include</em></a></td>
<td><a class="reference internal" href="jump.html"><em>jump</em></a></td>
<td><a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
<td><a class="reference internal" href="label.html"><em>label</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
<td><a class="reference internal" href="log.html"><em>log</em></a></td>
<td><a class="reference internal" href="mass.html"><em>mass</em></a></td>
<td><a class="reference internal" href="minimize.html"><em>minimize</em></a></td>
<td><a class="reference internal" href="min_modify.html"><em>min_modify</em></a></td>
<td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
<td><a class="reference internal" href="neb.html"><em>neb</em></a></td>
<td><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a></td>
<td><a class="reference internal" href="neighbor.html"><em>neighbor</em></a></td>
<td><a class="reference internal" href="newton.html"><em>newton</em></a></td>
<td><a class="reference internal" href="next.html"><em>next</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="package.html"><em>package</em></a></td>
<td><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></td>
<td><a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a></td>
<td><a class="reference internal" href="pair_style.html"><em>pair_style</em></a></td>
<td><a class="reference internal" href="pair_write.html"><em>pair_write</em></a></td>
<td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
<td><a class="reference internal" href="print.html"><em>print</em></a></td>
<td><a class="reference internal" href="processors.html"><em>processors</em></a></td>
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
<td><a class="reference internal" href="quit.html"><em>quit</em></a></td>
<td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
<td><a class="reference internal" href="read_restart.html"><em>read_restart</em></a></td>
<td><a class="reference internal" href="region.html"><em>region</em></a></td>
<td><a class="reference internal" href="replicate.html"><em>replicate</em></a></td>
<td><a class="reference internal" href="rerun.html"><em>rerun</em></a></td>
<td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
<td><a class="reference internal" href="run.html"><em>run</em></a></td>
<td><a class="reference internal" href="run_style.html"><em>run_style</em></a></td>
<td><a class="reference internal" href="set.html"><em>set</em></a></td>
<td><a class="reference internal" href="shell.html"><em>shell</em></a></td>
<td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
<td><a class="reference internal" href="tad.html"><em>tad</em></a></td>
<td><a class="reference internal" href="temper.html"><em>temper</em></a></td>
<td><a class="reference internal" href="thermo.html"><em>thermo</em></a></td>
<td><a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a></td>
<td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
<td><a class="reference internal" href="timestep.html"><em>timestep</em></a></td>
<td><a class="reference internal" href="uncompute.html"><em>uncompute</em></a></td>
<td><a class="reference internal" href="undump.html"><em>undump</em></a></td>
<td><a class="reference internal" href="unfix.html"><em>unfix</em></a></td>
<td><a class="reference internal" href="units.html"><em>units</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
<td><a class="reference internal" href="velocity.html"><em>velocity</em></a></td>
<td><a class="reference internal" href="write_data.html"><em>write_data</em></a></td>
<td><a class="reference internal" href="write_dump.html"><em>write_dump</em></a></td>
<td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional commands in USER packages, which can be used if
<a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="100%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="group2ndx.html"><em>group2ndx</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">
<h2>3.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="fix.html"><em>fix</em></a> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="11%" />
<col width="12%" />
<col width="13%" />
<col width="10%" />
<col width="11%" />
<col width="15%" />
<col width="12%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt.html"><em>adapt</em></a></td>
<td><a class="reference internal" href="fix_addforce.html"><em>addforce (c)</em></a></td>
<td><a class="reference internal" href="fix_append_atoms.html"><em>append/atoms</em></a></td>
<td><a class="reference internal" href="fix_atom_swap.html"><em>atom/swap</em></a></td>
<td><a class="reference internal" href="fix_aveforce.html"><em>aveforce (c)</em></a></td>
<td><a class="reference internal" href="fix_ave_atom.html"><em>ave/atom</em></a></td>
<td><a class="reference internal" href="fix_ave_chunk.html"><em>ave/chunk</em></a></td>
<td><a class="reference internal" href="fix_ave_correlate.html"><em>ave/correlate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo</em></a></td>
<td><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo/weight</em></a></td>
<td><a class="reference internal" href="fix_ave_spatial.html"><em>ave/spatial</em></a></td>
<td><a class="reference internal" href="fix_ave_time.html"><em>ave/time</em></a></td>
<td><a class="reference internal" href="fix_balance.html"><em>balance</em></a></td>
<td><a class="reference internal" href="fix_bond_break.html"><em>bond/break</em></a></td>
<td><a class="reference internal" href="fix_bond_create.html"><em>bond/create</em></a></td>
<td><a class="reference internal" href="fix_bond_swap.html"><em>bond/swap</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_box_relax.html"><em>box/relax</em></a></td>
<td><a class="reference internal" href="fix_deform.html"><em>deform (k)</em></a></td>
<td><a class="reference internal" href="fix_deposit.html"><em>deposit</em></a></td>
<td><a class="reference internal" href="fix_drag.html"><em>drag</em></a></td>
<td><a class="reference internal" href="fix_dt_reset.html"><em>dt/reset</em></a></td>
<td><a class="reference internal" href="fix_efield.html"><em>efield</em></a></td>
<td><a class="reference internal" href="fix_enforce2d.html"><em>enforce2d (c)</em></a></td>
<td><a class="reference internal" href="fix_evaporate.html"><em>evaporate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_external.html"><em>external</em></a></td>
<td><a class="reference internal" href="fix_freeze.html"><em>freeze (c)</em></a></td>
<td><a class="reference internal" href="fix_gcmc.html"><em>gcmc</em></a></td>
<td><a class="reference internal" href="fix_gld.html"><em>gld</em></a></td>
<td><a class="reference internal" href="fix_gravity.html"><em>gravity (co)</em></a></td>
<td><a class="reference internal" href="fix_heat.html"><em>heat</em></a></td>
<td><a class="reference internal" href="fix_indent.html"><em>indent</em></a></td>
<td><a class="reference internal" href="fix_langevin.html"><em>langevin (k)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_lineforce.html"><em>lineforce</em></a></td>
<td><a class="reference internal" href="fix_momentum.html"><em>momentum</em></a></td>
<td><a class="reference internal" href="fix_move.html"><em>move</em></a></td>
<td><a class="reference internal" href="fix_msst.html"><em>msst</em></a></td>
<td><a class="reference internal" href="fix_neb.html"><em>neb</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nph (ko)</em></a></td>
<td><a class="reference internal" href="fix_nphug.html"><em>nphug (o)</em></a></td>
<td><a class="reference internal" href="fix_nph_asphere.html"><em>nph/asphere (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nph_sphere.html"><em>nph/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>npt (cko)</em></a></td>
<td><a class="reference internal" href="fix_npt_asphere.html"><em>npt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_npt_sphere.html"><em>npt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve.html"><em>nve (cko)</em></a></td>
<td><a class="reference internal" href="fix_nve_asphere.html"><em>nve/asphere</em></a></td>
<td><a class="reference internal" href="fix_nve_asphere_noforce.html"><em>nve/asphere/noforce</em></a></td>
<td><a class="reference internal" href="fix_nve_body.html"><em>nve/body</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_limit.html"><em>nve/limit</em></a></td>
<td><a class="reference internal" href="fix_nve_line.html"><em>nve/line</em></a></td>
<td><a class="reference internal" href="fix_nve_noforce.html"><em>nve/noforce</em></a></td>
<td><a class="reference internal" href="fix_nve_sphere.html"><em>nve/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve_tri.html"><em>nve/tri</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nvt (cko)</em></a></td>
<td><a class="reference internal" href="fix_nvt_asphere.html"><em>nvt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_oneway.html"><em>oneway</em></a></td>
<td><a class="reference internal" href="fix_orient_fcc.html"><em>orient/fcc</em></a></td>
<td><a class="reference internal" href="fix_planeforce.html"><em>planeforce</em></a></td>
<td><a class="reference internal" href="fix_poems.html"><em>poems</em></a></td>
<td><a class="reference internal" href="fix_pour.html"><em>pour</em></a></td>
<td><a class="reference internal" href="fix_press_berendsen.html"><em>press/berendsen</em></a></td>
<td><a class="reference internal" href="fix_print.html"><em>print</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb (o)</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a></td>
<td><a class="reference internal" href="fix_recenter.html"><em>recenter</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_restrain.html"><em>restrain</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nph (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/npt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nve (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nvt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nph</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/npt</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nve</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nvt</em></a></td>
<td><a class="reference internal" href="fix_setforce.html"><em>setforce (c)</em></a></td>
<td><a class="reference internal" href="fix_shake.html"><em>shake (c)</em></a></td>
<td><a class="reference internal" href="fix_spring.html"><em>spring</em></a></td>
<td><a class="reference internal" href="fix_spring_rg.html"><em>spring/rg</em></a></td>
<td><a class="reference internal" href="fix_spring_self.html"><em>spring/self</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_srd.html"><em>srd</em></a></td>
<td><a class="reference internal" href="fix_store_force.html"><em>store/force</em></a></td>
<td><a class="reference internal" href="fix_store_state.html"><em>store/state</em></a></td>
<td><a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen (c)</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csld</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csvr</em></a></td>
<td><a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale (c)</em></a></td>
<td><a class="reference internal" href="fix_tfmc.html"><em>tfmc</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_thermal_conductivity.html"><em>thermal/conductivity</em></a></td>
<td><a class="reference internal" href="fix_tmd.html"><em>tmd</em></a></td>
<td><a class="reference internal" href="fix_ttm.html"><em>ttm</em></a></td>
<td><a class="reference internal" href="fix_tune_kspace.html"><em>tune/kspace</em></a></td>
<td><a class="reference internal" href="fix_vector.html"><em>vector</em></a></td>
<td><a class="reference internal" href="fix_viscosity.html"><em>viscosity</em></a></td>
<td><a class="reference internal" href="fix_viscous.html"><em>viscous (c)</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_wall_gran.html"><em>wall/gran</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/harmonic</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj1043</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a></td>
<td><a class="reference internal" href="fix_wall_piston.html"><em>wall/piston</em></a></td>
<td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect (k)</em></a></td>
<td><a class="reference internal" href="fix_wall_region.html"><em>wall/region</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_wall_srd.html"><em>wall/srd</em></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional fix styles in USER packages, which can be used if
<a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="14%" />
<col width="15%" />
<col width="15%" />
<col width="20%" />
<col width="14%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><em>adapt/fep</em></a></td>
<td><a class="reference internal" href="fix_addtorque.html"><em>addtorque</em></a></td>
<td><a class="reference internal" href="fix_atc.html"><em>atc</em></a></td>
<td><a class="reference internal" href="fix_ave_correlate_long.html"><em>ave/correlate/long</em></a></td>
<td><a class="reference internal" href="fix_ave_spatial_sphere.html"><em>ave/spatial/sphere</em></a></td>
<td><a class="reference internal" href="fix_drude.html"><em>drude</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/direct</em></a></td>
<td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/reverse</em></a></td>
<td><a class="reference internal" href="fix_colvars.html"><em>colvars</em></a></td>
<td><a class="reference internal" href="fix_gle.html"><em>gle</em></a></td>
<td><a class="reference internal" href="fix_imd.html"><em>imd</em></a></td>
<td><a class="reference internal" href="fix_ipi.html"><em>ipi</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_langevin_drude.html"><em>langevin/drude</em></a></td>
<td><a class="reference internal" href="fix_langevin_eff.html"><em>langevin/eff</em></a></td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>lb/fluid</em></a></td>
<td><a class="reference internal" href="fix_lb_momentum.html"><em>lb/momentum</em></a></td>
<td><a class="reference internal" href="fix_lb_pc.html"><em>lb/pc</em></a></td>
<td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><em>lb/rigid/pc/sphere</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_lb_viscous.html"><em>lb/viscous</em></a></td>
<td><a class="reference internal" href="fix_meso.html"><em>meso</em></a></td>
<td><a class="reference internal" href="fix_meso_stationary.html"><em>meso/stationary</em></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><em>nph/eff</em></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><em>npt/eff</em></a></td>
<td><a class="reference internal" href="fix_nve_eff.html"><em>nve/eff</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_nh_eff.html"><em>nvt/eff</em></a></td>
<td><a class="reference internal" href="fix_nvt_sllod_eff.html"><em>nvt/sllod/eff</em></a></td>
<td><a class="reference internal" href="fix_phonon.html"><em>phonon</em></a></td>
<td><a class="reference internal" href="fix_pimd.html"><em>pimd</em></a></td>
<td><a class="reference internal" href="fix_qbmsst.html"><em>qbmsst</em></a></td>
<td><a class="reference internal" href="fix_qeq_reax.html"><em>qeq/reax</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_qmmm.html"><em>qmmm</em></a></td>
<td><a class="reference internal" href="fix_qtb.html"><em>qtb</em></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/c/bonds</em></a></td>
<td><a class="reference internal" href="fix_reaxc_species.html"><em>reax/c/species</em></a></td>
<td><a class="reference internal" href="fix_saed_vtk.html"><em>saed/vtk</em></a></td>
<td><a class="reference internal" href="fix_smd.html"><em>smd</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_smd_adjust_dt.html"><em>smd/adjust/dt</em></a></td>
<td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><em>smd/integrate/tlsph</em></a></td>
<td><a class="reference internal" href="fix_smd_integrate_ulsph.html"><em>smd/integrate/ulsph</em></a></td>
<td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><em>smd/move/triangulated/surface</em></a></td>
<td><a class="reference internal" href="fix_smd_setvel.html"><em>smd/setvel</em></a></td>
<td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><em>smd/tlsph/reference/configuration</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_smd_wall_surface.html"><em>smd/wall/surface</em></a></td>
<td><a class="reference internal" href="fix_temp_rescale_eff.html"><em>temp/rescale/eff</em></a></td>
<td><a class="reference internal" href="fix_ti_rs.html"><em>ti/rs</em></a></td>
<td><a class="reference internal" href="fix_ti_spring.html"><em>ti/spring</em></a></td>
<td><a class="reference internal" href="fix_ttm.html"><em>ttm/mod</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="compute-styles">
<h2>3.7. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="compute.html"><em>compute</em></a> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="19%" />
<col width="17%" />
<col width="15%" />
<col width="17%" />
<col width="16%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
<td><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a></td>
<td><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a></td>
<td><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a></td>
<td><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a></td>
<td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
<td><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a></td>
<td><a class="reference internal" href="compute_com.html"><em>com</em></a></td>
<td><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a></td>
<td><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a></td>
<td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
<td><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a></td>
<td><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a></td>
<td><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a></td>
<td><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a></td>
<td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
<td><a class="reference internal" href="compute_erotate_sphere_atom.html"><em>erotate/sphere/atom</em></a></td>
<td><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a></td>
<td><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a></td>
<td><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a></td>
<td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
<td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td>
<td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td>
<td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td>
<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
<td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td>
<td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
<td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
<td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
<td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
<td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
<td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
<td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
<td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
<td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
<td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
<td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
<td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
</tr>
</tbody>
</table>
<p>These are additional compute styles in USER packages, which can be
used if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="17%" />
<col width="15%" />
<col width="19%" />
<col width="16%" />
<col width="15%" />
<col width="18%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_ackland_atom.html"><em>ackland/atom</em></a></td>
<td><a class="reference internal" href="compute_basal_atom.html"><em>basal/atom</em></a></td>
<td><a class="reference internal" href="compute_fep.html"><em>fep</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>force/tally</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>heat/flux/tally</em></a></td>
<td><a class="reference internal" href="compute_ke_eff.html"><em>ke/eff</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_ke_atom_eff.html"><em>ke/atom/eff</em></a></td>
<td><a class="reference internal" href="compute_meso_e_atom.html"><em>meso_e/atom</em></a></td>
<td><a class="reference internal" href="compute_meso_rho_atom.html"><em>meso_rho/atom</em></a></td>
<td><a class="reference internal" href="compute_meso_t_atom.html"><em>meso_t/atom</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>pe/tally</em></a></td>
<td><a class="reference internal" href="compute_saed.html"><em>saed</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_smd_contact_radius.html"><em>smd/contact/radius</em></a></td>
<td><a class="reference internal" href="compute_smd_damage.html"><em>smd/damage</em></a></td>
<td><a class="reference internal" href="compute_smd_hourglass_error.html"><em>smd/hourglass/error</em></a></td>
<td><a class="reference internal" href="compute_smd_internal_energy.html"><em>smd/internal/energy</em></a></td>
<td><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic/strain</em></a></td>
<td><a class="reference internal" href="compute_smd_plastic_strain_rate.html"><em>smd/plastic/strain/rate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_smd_rho.html"><em>smd/rho</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_defgrad.html"><em>smd/tlsph/defgrad</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_dt.html"><em>smd/tlsph/dt</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_num_neighs.html"><em>smd/tlsph/num/neighs</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_shape.html"><em>smd/tlsph/shape</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph/strain</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph/strain/rate</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph/stress</em></a></td>
<td><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html"><em>smd/triangle/mesh/vertices</em></a></td>
<td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td>
<td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td>
<td><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_smd_ulsph_stress.html"><em>smd/ulsph/stress</em></a></td>
<td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>stress/tally</em></a></td>
<td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
<td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_rotate.html"><em>temp/rotate</em></a></td>
<td><a class="reference internal" href="compute_xrd.html"><em>xrd</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="pair-style-potentials">
<h2>3.8. Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="24%" />
<col width="25%" />
<col width="27%" />
<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a></td>
<td><a class="reference internal" href="pair_adp.html"><em>adp (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_airebo.html"><em>airebo (o)</em></a></td>
<td><a class="reference internal" href="pair_beck.html"><em>beck (go)</em></a></td>
<td><a class="reference internal" href="pair_body.html"><em>body</em></a></td>
<td><a class="reference internal" href="pair_bop.html"><em>bop</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><em>born (go)</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long (cgo)</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/msm (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born/coul/wolf (go)</em></a></td>
<td><a class="reference internal" href="pair_brownian.html"><em>brownian (o)</em></a></td>
<td><a class="reference internal" href="pair_brownian.html"><em>brownian/poly (o)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck (cgko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck/coul/cut (cgko)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long (cgko)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/msm (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_buck_long.html"><em>buck/long/coul/long (o)</em></a></td>
<td><a class="reference internal" href="pair_colloid.html"><em>colloid (go)</em></a></td>
<td><a class="reference internal" href="pair_comb.html"><em>comb (o)</em></a></td>
<td><a class="reference internal" href="pair_comb.html"><em>comb3</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/cut (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/debye (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/dsf (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/long (gko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/msm</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/streitz</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/wolf (ko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dpd.html"><em>dpd (o)</em></a></td>
<td><a class="reference internal" href="pair_dpd.html"><em>dpd/tstat (o)</em></a></td>
<td><a class="reference internal" href="pair_dsmc.html"><em>dsmc</em></a></td>
<td><a class="reference internal" href="pair_eam.html"><em>eam (cgkot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam/alloy (cgkot)</em></a></td>
<td><a class="reference internal" href="pair_eam.html"><em>eam/fs (cgkot)</em></a></td>
<td><a class="reference internal" href="pair_eim.html"><em>eim (o)</em></a></td>
<td><a class="reference internal" href="pair_gauss.html"><em>gauss (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_gayberne.html"><em>gayberne (gio)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hertz/history (o)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke (co)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke/history (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/morse (o)</em></a></td>
<td><a class="reference internal" href="pair_kim.html"><em>kim</em></a></td>
<td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_line_lj.html"><em>line/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm/implicit (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/msm</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2 (cgko)</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/cut (cko)</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/long (cgko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_cubic.html"><em>lj/cubic (go)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut (cgikot)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/cut (cgko)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/debye (cgko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long (cgikot)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs/coul/gromacs (cko)</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/tip4p/long</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth.html"><em>lj/smooth (co)</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate/poly (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
<td><a class="reference internal" href="pair_meam.html"><em>meam (o)</em></a></td>
<td><a class="reference internal" href="pair_mie.html"><em>mie/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/lps (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/pmb (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
<td><a class="reference internal" href="pair_reax.html"><em>reax</em></a></td>
<td><a class="reference internal" href="pair_airebo.html"><em>rebo (o)</em></a></td>
<td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
<td><a class="reference internal" href="pair_soft.html"><em>soft (go)</em></a></td>
<td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
<td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_vashishta.html"><em>vashishta (o)</em></a></td>
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
<td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional pair styles in USER packages, which can be used
if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
+<col width="21%" />
<col width="25%" />
-<col width="29%" />
-<col width="22%" />
-<col width="24%" />
+<col width="31%" />
+<col width="23%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><em>awpmd/cut</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>coul/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_coul_diel.html"><em>coul/diel (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>coul/long/soft (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam/cd (o)</em></a></td>
<td><a class="reference internal" href="pair_edip.html"><em>edip (o)</em></a></td>
<td><a class="reference internal" href="pair_eff.html"><em>eff/cut</em></a></td>
<td><a class="reference internal" href="pair_gauss.html"><em>gauss/cut</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_list.html"><em>list</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/long/soft (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/sf (go)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk (gko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/long (go)</em></a></td>
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
<td><a class="reference internal" href="pair_meam_spline.html"><em>meam/spline</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_meam_sw_spline.html"><em>meam/sw/spline</em></a></td>
+<td><a class="reference internal" href="pair_mgpt.html"><em>mgpt</em></a></td>
<td><a class="reference internal" href="pair_quip.html"><em>quip</em></a></td>
<td><a class="reference internal" href="pair_reax_c.html"><em>reax/c</em></a></td>
-<td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
+<td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
<td><a class="reference internal" href="pair_smd_triangulated_surface.html"><em>smd/triangulated/surface</em></a></td>
<td><a class="reference internal" href="pair_smd_ulsph.html"><em>smd/ulsph</em></a></td>
-<td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_smtbq.html"><em>smtbq</em></a></td>
+<td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
+<td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
<td><a class="reference internal" href="pair_sph_lj.html"><em>sph/lj</em></a></td>
-<td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
-<td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
+<td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
+<td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
<td><a class="reference internal" href="pair_srp.html"><em>srp</em></a></td>
-<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
-<td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
-<td> </td>
-<td> </td>
+<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
+<td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
+<td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="bond-style-potentials">
<h2>3.9. Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="28%" />
<col width="25%" />
<col width="22%" />
<col width="25%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="bond_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="bond_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="bond_class2.html"><em>class2 (o)</em></a></td>
<td><a class="reference internal" href="bond_fene.html"><em>fene (ko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="bond_fene_expand.html"><em>fene/expand (o)</em></a></td>
<td><a class="reference internal" href="bond_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="bond_morse.html"><em>morse (o)</em></a></td>
<td><a class="reference internal" href="bond_nonlinear.html"><em>nonlinear (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="bond_quartic.html"><em>quartic (o)</em></a></td>
<td><a class="reference internal" href="bond_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional bond styles in USER packages, which can be used
if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="46%" />
<col width="54%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="bond_harmonic_shift.html"><em>harmonic/shift (o)</em></a></td>
<td><a class="reference internal" href="bond_harmonic_shift_cut.html"><em>harmonic/shift/cut (o)</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="angle-style-potentials">
<h2>3.10. Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="angle_style.html"><em>angle_style</em></a> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="25%" />
<col width="28%" />
<col width="27%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="angle_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="angle_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="angle_class2.html"><em>class2 (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="angle_cosine.html"><em>cosine (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_delta.html"><em>cosine/delta (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_periodic.html"><em>cosine/periodic (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="angle_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional angle styles in USER packages, which can be used
if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="29%" />
<col width="31%" />
<col width="20%" />
<col width="21%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_cosine_shift.html"><em>cosine/shift (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_shift_exp.html"><em>cosine/shift/exp (o)</em></a></td>
<td><a class="reference internal" href="angle_dipole.html"><em>dipole (o)</em></a></td>
<td><a class="reference internal" href="angle_fourier.html"><em>fourier (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="angle_fourier_simple.html"><em>fourier/simple (o)</em></a></td>
<td><a class="reference internal" href="angle_quartic.html"><em>quartic (o)</em></a></td>
<td><a class="reference internal" href="angle_sdk.html"><em>sdk</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="dihedral-style-potentials">
<h2>3.11. Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="25%" />
<col width="21%" />
<col width="32%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="dihedral_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="dihedral_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="dihedral_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_helix.html"><em>helix (o)</em></a></td>
<td><a class="reference internal" href="dihedral_multi_harmonic.html"><em>multi/harmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_opls.html"><em>opls (ko)</em></a></td>
</tr>
</tbody>
</table>
<p>These are additional dihedral styles in USER packages, which can be
used if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="31%" />
<col width="21%" />
<col width="24%" />
<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="dihedral_cosine_shift_exp.html"><em>cosine/shift/exp (o)</em></a></td>
<td><a class="reference internal" href="dihedral_fourier.html"><em>fourier (o)</em></a></td>
<td><a class="reference internal" href="dihedral_nharmonic.html"><em>nharmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_quadratic.html"><em>quadratic (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dihedral_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="improper-style-potentials">
<h2>3.12. Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="improper_style.html"><em>improper_style</em></a> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="27%" />
<col width="24%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="improper_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="improper_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="improper_class2.html"><em>class2 (o)</em></a></td>
<td><a class="reference internal" href="improper_cvff.html"><em>cvff (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="improper_umbrella.html"><em>umbrella (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional improper styles in USER packages, which can be
used if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="33%" />
<col width="36%" />
<col width="31%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="improper_cossq.html"><em>cossq (o)</em></a></td>
<td><a class="reference internal" href="improper_fourier.html"><em>fourier (o)</em></a></td>
<td><a class="reference internal" href="improper_ring.html"><em>ring (o)</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="kspace-solvers">
<h2>3.13. Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="24%" />
<col width="23%" />
<col width="27%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>ewald (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>ewald/disp</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>msm (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>msm/cg (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="kspace_style.html"><em>pppm (cgo)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/cg (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp/tip4p</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>pppm/tip4p (o)</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_packages.html" class="btn btn-neutral float-right" title="4. Packages" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_start.html" class="btn btn-neutral" title="2. Getting Started" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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\ No newline at end of file
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index c5aad509a..f8c0c7630 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -1,1079 +1,1081 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
3. Commands :h3
This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
:line
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
timestep 0.5
run 100
run 100 :pre
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
"read_data"_read_data.html command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. "This section"_Section_errors.html gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
Here is how each line in the input script is parsed by LAMMPS:
(1) If the last printable character on the line is a "&" character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the "&" character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using "&" characters.
(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
"x".
How the variable is converted to a text string depends on what style
of variable it is; see the "variable"_variable doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an "equal-style variable"_variable.html. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete :pre
can be replaced by
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
so that you do not have to define (or discard) a temporary variable X.
Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
variable a equal 2
variable b2 equal 4
print "B2 = $\{b$a\}" :pre
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
"equal-style variable"_variable.html.
See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the "&" character is used, as described above. When
the lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
print "Volume = $v"
print 'Volume = $v'
if "$\{steps\} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
""" :pre
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
See the "dump modify format"_dump_modify.html, "print"_print.html,
"if"_if.html, and "python"_python.html commands for examples.
A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"Section_example"_Section_example.html, and animated on the "LAMMPS
WWW Site"_lws.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.
:line
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
"boundary"_boundary.html, "dimension"_dimension.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html
Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html,
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
"region"_region.html, "replicate"_replicate.html
Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.html,
"special_bonds"_special_bonds.html
Settings:
"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
"restart"_restart.html, "thermo"_thermo.html,
"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
"undump"_undump.html, "write_data"_write_data.html,
"write_dump"_write_dump.html, "write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
Miscellaneous:
"clear"_clear.html, "echo"_echo.html, "if"_if.html,
"include"_include.html, "jump"_jump.html, "label"_label.html,
"log"_log.html, "next"_next.html, "print"_print.html,
"shell"_shell.html, "variable"_variable.html
:line
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"molecule"_molecule.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"python"_python.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
These are additional commands in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"group2ndx"_group2ndx.html :tb(c=1,ea=c)
:line
Fix styles :h4
See the "fix"_fix.html command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the "appropriate accelerated package"_Section_accelerate.html.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"adapt"_fix_adapt.html,
"addforce (c)"_fix_addforce.html,
"append/atoms"_fix_append_atoms.html,
"atom/swap"_fix_atom_swap.html,
"aveforce (c)"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/chunk"_fix_ave_chunk.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/histo/weight"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"balance"_fix_balance.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d (c)"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze (c)"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gravity (co)"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin (k)"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"momentum"_fix_momentum.html,
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph (ko)"_fix_nh.html,
"nphug (o)"_fix_nphug.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/sphere (o)"_fix_nph_sphere.html,
"npt (cko)"_fix_nh.html,
"npt/asphere (o)"_fix_npt_asphere.html,
"npt/sphere (o)"_fix_npt_sphere.html,
"nve (cko)"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/body"_fix_nve_body.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere (o)"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt (cko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
"nvt/sllod (o)"_fix_nvt_sllod.html,
"nvt/sphere (o)"_fix_nvt_sphere.html,
"oneway"_fix_oneway.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom"_fix_property_atom.html,
"qeq/comb (o)"_fix_qeq_comb.html,
"qeq/dynamic"_fix_qeq.html,
"qeq/point"_fix_qeq.html,
"qeq/shielded"_fix_qeq.html,
"qeq/slater"_fix_qeq.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid (o)"_fix_rigid.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
"rigid/small (o)"_fix_rigid.html,
"rigid/small/nph"_fix_rigid.html,
"rigid/small/npt"_fix_rigid.html,
"rigid/small/nve"_fix_rigid.html,
"rigid/small/nvt"_fix_rigid.html,
"setforce (c)"_fix_setforce.html,
"shake (c)"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen (c)"_fix_temp_berendsen.html,
"temp/csld"_fix_temp_csvr.html,
"temp/csvr"_fix_temp_csvr.html,
"temp/rescale (c)"_fix_temp_rescale.html,
"tfmc"_fix_tfmc.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"tune/kspace"_fix_tune_kspace.html,
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous (c)"_fix_viscous.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are additional fix styles in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"adapt/fep"_fix_adapt_fep.html,
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
"ave/spatial/sphere"_fix_ave_spatial_sphere.html,
"drude"_fix_drude.html,
"drude/transform/direct"_fix_drude_transform.html,
"drude/transform/reverse"_fix_drude_transform.html,
"colvars"_fix_colvars.html,
"gle"_fix_gle.html,
"imd"_fix_imd.html,
"ipi"_fix_ipi.html,
"langevin/drude"_fix_langevin_drude.html,
"langevin/eff"_fix_langevin_eff.html,
"lb/fluid"_fix_lb_fluid.html,
"lb/momentum"_fix_lb_momentum.html,
"lb/pc"_fix_lb_pc.html,
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
"lb/viscous"_fix_lb_viscous.html,
"meso"_fix_meso.html,
"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"phonon"_fix_phonon.html,
"pimd"_fix_pimd.html,
"qbmsst"_fix_qbmsst.html,
"qeq/reax"_fix_qeq_reax.html,
"qmmm"_fix_qmmm.html,
"qtb"_fix_qtb.html,
"reax/c/bonds"_fix_reaxc_bonds.html,
"reax/c/species"_fix_reaxc_species.html,
"saed/vtk"_fix_saed_vtk.html,
"smd"_fix_smd.html,
"smd/adjust/dt"_fix_smd_adjust_dt.html,
"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
"smd/setvel"_fix_smd_setvel.html,
"smd/tlsph/reference/configuration"_fix_smd_tlsph_reference_configuration.html,
"smd/wall/surface"_fix_smd_wall_surface.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"ti/rs"_fix_ti_rs.html,
"ti/spring"_fix_ti_spring.html,
"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
:line
Compute styles :h4
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"angle/local"_compute_angle_local.html,
"angmom/chunk"_compute_angmom_chunk.html,
"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/chunk"_compute_com_chunk.html,
"contact/atom"_compute_contact_atom.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
"dilatation/atom"_compute_dilatation_atom.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/rigid"_compute_erotate_rigid.html,
"erotate/sphere"_compute_erotate_sphere.html,
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
"event/displace"_compute_event_displace.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/chunk"_compute_gyration_chunk.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"inertia/chunk"_compute_inertia_chunk.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"ke/rigid"_compute_ke_rigid.html,
"msd"_compute_msd.html,
"msd/chunk"_compute_msd_chunk.html,
"msd/nongauss"_compute_msd_nongauss.html,
"omega/chunk"_compute_omega_chunk.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe (c)"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"plasticity/atom"_compute_plasticity_atom.html,
"pressure (c)"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/chunk"_compute_property_chunk.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
"slice"_compute_slice.html,
"sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,
"stress/atom"_compute_stress_atom.html,
"temp (ck)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/chunk"_compute_temp_chunk.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial (c)"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html,
"ti"_compute_ti.html,
"torque/chunk"_compute_torque_chunk.html,
"vacf"_compute_vacf.html,
"vcm/chunk"_compute_vcm_chunk.html,
"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
These are additional compute styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ackland/atom"_compute_ackland_atom.html,
"basal/atom"_compute_basal_atom.html,
"fep"_compute_fep.html,
"force/tally"_compute_tally.html,
"heat/flux/tally"_compute_tally.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"meso_e/atom"_compute_meso_e_atom.html,
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"pe/tally"_compute_tally.html,
"saed"_compute_saed.html,
"smd/contact/radius"_compute_smd_contact_radius.html,
"smd/damage"_compute_smd_damage.html,
"smd/hourglass/error"_compute_smd_hourglass_error.html,
"smd/internal/energy"_compute_smd_internal_energy.html,
"smd/plastic/strain"_compute_smd_plastic_strain.html,
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
"smd/rho"_compute_smd_rho.html,
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html,
"stress/tally"_compute_tally.html,
"temp/drude"_compute_temp_drude.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html,
"xrd"_compute_xrd.html :tb(c=6,ea=c)
:line
Pair_style potentials :h4
See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"adp (o)"_pair_adp.html,
"airebo (o)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/long (cgo)"_pair_born.html,
"born/coul/long/cs"_pair_born.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (cgko)"_pair_buck.html,
"buck/coul/cut (cgko)"_pair_buck.html,
"buck/coul/long (cgko)"_pair_buck.html,
"buck/coul/long/cs"_pair_buck.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
"colloid (go)"_pair_colloid.html,
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
"coul/cut (gko)"_pair_coul.html,
"coul/debye (gko)"_pair_coul.html,
"coul/dsf (gko)"_pair_coul.html,
"coul/long (gko)"_pair_coul.html,
"coul/long/cs"_pair_coul.html,
"coul/msm"_pair_coul.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"dpd (o)"_pair_dpd.html,
"dpd/tstat (o)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam (cgkot)"_pair_eam.html,
"eam/alloy (cgkot)"_pair_eam.html,
"eam/fs (cgkot)"_pair_eam.html,
"eim (o)"_pair_eim.html,
"gauss (go)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (co)"_pair_gran.html,
"gran/hooke/history (o)"_pair_gran.html,
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
"kim"_pair_kim.html,
"lcbop"_pair_lcbop.html,
"line/lj (o)"_pair_line_lj.html,
"lj/charmm/coul/charmm (cko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (cko)"_pair_charmm.html,
"lj/charmm/coul/long (cgiko)"_pair_charmm.html,
"lj/charmm/coul/msm"_pair_charmm.html,
"lj/class2 (cgko)"_pair_class2.html,
"lj/class2/coul/cut (cko)"_pair_class2.html,
"lj/class2/coul/long (cgko)"_pair_class2.html,
"lj/cubic (go)"_pair_lj_cubic.html,
"lj/cut (cgikot)"_pair_lj.html,
"lj/cut/coul/cut (cgko)"_pair_lj.html,
"lj/cut/coul/debye (cgko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (cgikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
"lj/cut/tip4p/long (ot)"_pair_lj.html,
"lj/expand (cgko)"_pair_lj_expand.html,
"lj/gromacs (cgko)"_pair_gromacs.html,
"lj/gromacs/coul/gromacs (cko)"_pair_gromacs.html,
"lj/long/coul/long (o)"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/smooth (co)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj96/cut (cgo)"_pair_lj96.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"meam (o)"_pair_meam.html,
"mie/cut (o)"_pair_mie.html,
"morse (cgot)"_pair_morse.html,
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,
"peri/eps"_pair_peri.html,
"peri/lps (o)"_pair_peri.html,
"peri/pmb (o)"_pair_peri.html,
"peri/ves"_pair_peri.html,
"polymorphic"_pair_polymorphic.html,
"rebo (o)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"snap"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (cgkio)"_pair_sw.html,
"table (gko)"_pair_table.html,
"tersoff (cgko)"_pair_tersoff.html,
"tersoff/mod (ko)"_pair_tersoff_mod.html,
"tersoff/zbl (ko)"_pair_tersoff_zbl.html,
"tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html,
"tri/lj (o)"_pair_tri_lj.html,
"vashishta (o)"_pair_vashishta.html,
"yukawa (go)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
These are additional pair styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"coul/cut/soft (o)"_pair_lj_soft.html,
"coul/diel (o)"_pair_coul_diel.html,
"coul/long/soft (o)"_pair_lj_soft.html,
"eam/cd (o)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"eff/cut"_pair_eff.html,
"gauss/cut"_pair_gauss.html,
"list"_pair_list.html,
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
"lj/sdk (gko)"_pair_sdk.html,
"lj/sdk/coul/long (go)"_pair_sdk.html,
"lj/sdk/coul/msm (o)"_pair_sdk.html,
"lj/sf (o)"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
+"mgpt"_pair_mgpt.html,
"quip"_pair_quip.html,
"reax/c"_pair_reax_c.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
"sph/lj"_pair_sph_lj.html,
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"srp"_pair_srp.html,
"tersoff/table (o)"_pair_tersoff.html,
"thole"_pair_thole.html,
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
:line
Bond_style potentials :h4
See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_bond_none.html,
"hybrid"_bond_hybrid.html,
"class2 (o)"_bond_class2.html,
"fene (ko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"harmonic (ko)"_bond_harmonic.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"quartic (o)"_bond_quartic.html,
"table (o)"_bond_table.html :tb(c=4,ea=c)
These are additional bond styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
:line
Angle_style potentials :h4
See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_angle_none.html,
"hybrid"_angle_hybrid.html,
"charmm (ko)"_angle_charmm.html,
"class2 (o)"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"harmonic (ko)"_angle_harmonic.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
These are additional angle styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"quartic (o)"_angle_quartic.html,
"sdk"_angle_sdk.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h4
See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_dihedral_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html,
"class2 (o)"_dihedral_class2.html,
"harmonic (o)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"opls (ko)"_dihedral_opls.html :tb(c=4,ea=c)
These are additional dihedral styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (o)"_dihedral_fourier.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"table (o)"_dihedral_table.html :tb(c=4,ea=c)
:line
Improper_style potentials :h4
See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2 (o)"_improper_class2.html,
"cvff (o)"_improper_cvff.html,
"harmonic (ko)"_improper_harmonic.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
These are additional improper styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cossq (o)"_improper_cossq.html,
"fourier (o)"_improper_fourier.html,
"ring (o)"_improper_ring.html :tb(c=4,ea=c)
:line
Kspace solvers :h4
See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"ewald (o)"_kspace_style.html,
"ewald/disp"_kspace_style.html,
"msm (o)"_kspace_style.html,
"msm/cg (o)"_kspace_style.html,
"pppm (cgo)"_kspace_style.html,
"pppm/cg (o)"_kspace_style.html,
"pppm/disp"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index eaa221f45..7e8f53434 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -1,1521 +1,1591 @@
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<title>4. Packages — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.13. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.14. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.15. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.25. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.26. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.27. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.28. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.29. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.30. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.31. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.32. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.33. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.34. USER-SPH package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.26. USER-MGPT package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.27. USER-MISC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.28. USER-MOLFILE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.29. USER-OMP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.30. USER-PHONON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.31. USER-QMMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.32. USER-QTB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.33. USER-REAXC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.34. USER-SMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.36. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
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<div class="section" id="packages">
<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
<p>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.</p>
<div class="line-block">
<div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
<div class="line"><br /></div>
</div>
<p>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing “make package” from within the src
directory of the LAMMPS distribution.</p>
<p>See <a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.</p>
<p>Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
packages include commands derived from commands in other packages. If
the other package is not installed, the derived command from the new
package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE pacakge and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
<p>The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sections below give a few more
details, including instructions for building LAMMPS with the package,
either via the make command or the Make.py tool described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a>.</p>
<div class="section" id="standard-packages">
<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
<p>The current list of standard packages is as follows.</p>
<table border="1" class="docutils">
<colgroup>
<col width="7%" />
<col width="23%" />
<col width="24%" />
<col width="32%" />
<col width="7%" />
<col width="7%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Library</td>
</tr>
<tr class="row-even"><td>ASPHERE</td>
<td>aspherical particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 6.14</span></a></td>
<td>ellipse</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>BODY</td>
<td>body-style particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="body.html"><em>body</em></a></td>
<td>body</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>CLASS2</td>
<td>class 2 force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>COLLOID</td>
<td>colloidal particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="atom_style.html"><em>atom_style colloid</em></a></td>
<td>colloid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>COMPRESS</td>
<td>I/O compression</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump.html"><em>dump */gz</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>CORESHELL</td>
<td>adiabatic core/shell model</td>
<td>Hendrik Heenen (Technical U of Munich)</td>
<td><a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 6.25</span></a></td>
<td>coreshell</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>DIPOLE</td>
<td>point dipole particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_dipole.html"><em>pair_style dipole/cut</em></a></td>
<td>dipole</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>FLD</td>
<td>Fast Lubrication Dynamics</td>
<td>Kumar & Bybee & Higdon (1)</td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>GPU</td>
<td>GPU-enabled styles</td>
<td>Mike Brown (ORNL)</td>
<td><a class="reference internal" href="accelerate_gpu.html"><em>Section accelerate</em></a></td>
<td>gpu</td>
<td>lib/gpu</td>
</tr>
<tr class="row-odd"><td>GRANULAR</td>
<td>granular systems</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-6"><span>Section_howto 6.6</span></a></td>
<td>pour</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>KIM</td>
<td>openKIM potentials</td>
<td>Smirichinski & Elliot & Tadmor (3)</td>
<td><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a></td>
<td>kim</td>
<td>KIM</td>
</tr>
<tr class="row-odd"><td>KOKKOS</td>
<td>Kokkos-enabled styles</td>
<td>Trott & Edwards (4)</td>
<td><a class="reference internal" href="accelerate_kokkos.html"><em>Section_accelerate</em></a></td>
<td>kokkos</td>
<td>lib/kokkos</td>
</tr>
<tr class="row-even"><td>KSPACE</td>
<td>long-range Coulombic solvers</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>MANYBODY</td>
<td>many-body potentials</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a></td>
<td>shear</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>MEAM</td>
<td>modified EAM potential</td>
<td>Greg Wagner (Sandia)</td>
<td><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></td>
<td>meam</td>
<td>lib/meam</td>
</tr>
<tr class="row-odd"><td>MC</td>
<td>Monte Carlo options</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>MOLECULE</td>
<td>molecular system force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-3"><span>Section_howto 6.3</span></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>OPT</td>
<td>optimized pair styles</td>
<td>Fischer & Richie & Natoli (2)</td>
<td><a class="reference internal" href="accelerate_opt.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>PERI</td>
<td>Peridynamics models</td>
<td>Mike Parks (Sandia)</td>
<td><a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a></td>
<td>peri</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>POEMS</td>
<td>coupled rigid body motion</td>
<td>Rudra Mukherjee (JPL)</td>
<td><a class="reference internal" href="fix_poems.html"><em>fix poems</em></a></td>
<td>rigid</td>
<td>lib/poems</td>
</tr>
<tr class="row-even"><td>PYTHON</td>
<td>embed Python code in an input script</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
<td>python</td>
<td>lib/python</td>
</tr>
<tr class="row-odd"><td>REAX</td>
<td>ReaxFF potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
<td>reax</td>
<td>lib/reax</td>
</tr>
<tr class="row-even"><td>REPLICA</td>
<td>multi-replica methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 6.5</span></a></td>
<td>tad</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>RIGID</td>
<td>rigid bodies</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a></td>
<td>rigid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>SHOCK</td>
<td>shock loading methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_msst.html"><em>fix msst</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>SNAP</td>
<td>quantum-fit potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_snap.html"><em>pair snap</em></a></td>
<td>snap</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>SRD</td>
<td>stochastic rotation dynamics</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_srd.html"><em>fix srd</em></a></td>
<td>srd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>VORONOI</td>
<td>Voronoi tesselations</td>
<td>Daniel Schwen (LANL)</td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>Voro++</td>
</tr>
<tr class="row-even"><td>XTC</td>
<td>dumps in XTC format</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
responible for creating and maintaining the package.
More details on
multiple authors are give below.</p>
<p>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon’s group at UIUC.</p>
<p>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).</p>
<p>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).</p>
<p>(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.</p>
<p>The “Doc page” column links to either a portion of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. <a class="reference internal" href="Section_start.html#start-3-3"><span>Section start</span></a> of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.</p>
<p>Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-package
make machine
or
Make.py -p package -a machine
</pre></div>
</div>
<p>To un-install the package and re-build LAMMPS without it:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-package
make machine
or
Make.py -p ^package -a machine
</pre></div>
</div>
<p>“Package” is the name of the package in lower-case letters,
e.g. asphere or rigid, and “machine” is the build target, e.g. mpi or
serial.</p>
</div>
<div class="section" id="build-instructions-for-compress-package">
<h2>4.2. Build instructions for COMPRESS package<a class="headerlink" href="#build-instructions-for-compress-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-gpu-package">
<h2>4.3. Build instructions for GPU package<a class="headerlink" href="#build-instructions-for-gpu-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-kim-package">
<h2>4.4. Build instructions for KIM package<a class="headerlink" href="#build-instructions-for-kim-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-kokkos-package">
<h2>4.5. Build instructions for KOKKOS package<a class="headerlink" href="#build-instructions-for-kokkos-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-kspace-package">
<h2>4.6. Build instructions for KSPACE package<a class="headerlink" href="#build-instructions-for-kspace-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-meam-package">
<h2>4.7. Build instructions for MEAM package<a class="headerlink" href="#build-instructions-for-meam-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-poems-package">
<h2>4.8. Build instructions for POEMS package<a class="headerlink" href="#build-instructions-for-poems-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-python-package">
<h2>4.9. Build instructions for PYTHON package<a class="headerlink" href="#build-instructions-for-python-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-reax-package">
<h2>4.10. Build instructions for REAX package<a class="headerlink" href="#build-instructions-for-reax-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-voronoi-package">
<h2>4.11. Build instructions for VORONOI package<a class="headerlink" href="#build-instructions-for-voronoi-package" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="build-instructions-for-xtc-package">
<h2>4.12. Build instructions for XTC package<a class="headerlink" href="#build-instructions-for-xtc-package" title="Permalink to this headline">¶</a></h2>
<hr class="docutils" />
</div>
<div class="section" id="user-packages">
<span id="pkg-2"></span><h2>4.13. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
<p>The current list of user-contributed packages is as follows:</p>
<table border="1" class="docutils">
<colgroup>
<col width="8%" />
<col width="21%" />
<col width="22%" />
<col width="25%" />
<col width="8%" />
<col width="10%" />
<col width="6%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Pic/movie</td>
<td>Library</td>
</tr>
<tr class="row-even"><td>USER-ATC</td>
<td>atom-to-continuum coupling</td>
<td>Jones & Templeton & Zimmerman (1)</td>
<td><a class="reference internal" href="fix_atc.html"><em>fix atc</em></a></td>
<td>USER/atc</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#atc">atc</a></td>
<td>lib/atc</td>
</tr>
<tr class="row-odd"><td>USER-AWPMD</td>
<td>wave-packet MD</td>
<td>Ilya Valuev (JIHT)</td>
<td><a class="reference internal" href="pair_awpmd.html"><em>pair_style awpmd/cut</em></a></td>
<td>USER/awpmd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/awpmd</td>
</tr>
<tr class="row-even"><td>USER-CG-CMM</td>
<td>coarse-graining model</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a></td>
<td>USER/cg-cmm</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#cg">cg</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-COLVARS</td>
<td>collective variables</td>
<td>Fiorin & Henin & Kohlmeyer (2)</td>
<td><a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></td>
<td>USER/colvars</td>
<td><a class="reference external" href="colvars">colvars</a></td>
<td>lib/colvars</td>
</tr>
<tr class="row-even"><td>USER-CUDA</td>
<td>NVIDIA GPU styles</td>
<td>Christian Trott (U Tech Ilmenau)</td>
<td><a class="reference internal" href="accelerate_cuda.html"><em>Section accelerate</em></a></td>
<td>USER/cuda</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/cuda</td>
</tr>
<tr class="row-odd"><td>USER-DIFFRACTION</td>
<td>virutal x-ray and electron diffraction</td>
<td>Shawn Coleman (ARL)</td>
<td><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></td>
<td>USER/diffraction</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-DRUDE</td>
<td>Drude oscillators</td>
<td>Dequidt & Devemy & Padua (3)</td>
<td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
<td>USER/drude</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-EFF</td>
<td>electron force field</td>
<td>Andres Jaramillo-Botero (Caltech)</td>
<td><a class="reference internal" href="pair_eff.html"><em>pair_style eff/cut</em></a></td>
<td>USER/eff</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#eff">eff</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-FEP</td>
<td>free energy perturbation</td>
<td>Agilio Padua (U Blaise Pascal Clermont-Ferrand)</td>
<td><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></td>
<td>USER/fep</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-H5MD</td>
<td>dump output via HDF5</td>
<td>Pierre de Buyl (KU Leuven)</td>
<td><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/h5md</td>
</tr>
<tr class="row-even"><td>USER-INTEL</td>
<td>Vectorized CPU and Intel(R) coprocessor styles</td>
<td><ol class="first last upperalpha simple" start="23">
<li>Michael Brown (Intel)</li>
</ol>
</td>
<td><a class="reference internal" href="accelerate_intel.html"><em>Section accelerate</em></a></td>
<td>examples/intel</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-LB</td>
<td>Lattice Boltzmann fluid</td>
<td>Colin Denniston (U Western Ontario)</td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></td>
<td>USER/lb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-even"><td>USER-MISC</td>
+<tr class="row-even"><td>USER-MGPT</td>
+<td>fast MGPT multi-ion potentials</td>
+<td>Tomas Oppelstrup & John Moriarty (LLNL)</td>
+<td><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></td>
+<td>USER/mgpt</td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+</tr>
+<tr class="row-odd"><td>USER-MISC</td>
<td>single-file contributions</td>
<td>USER-MISC/README</td>
<td>USER-MISC/README</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-odd"><td>USER-MOLFILE</td>
+<tr class="row-even"><td>USER-MOLFILE</td>
<td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molfile plug-ins</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>VMD-MOLFILE</td>
</tr>
-<tr class="row-even"><td>USER-OMP</td>
+<tr class="row-odd"><td>USER-OMP</td>
<td>OpenMP threaded styles</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="accelerate_omp.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-odd"><td>USER-PHONON</td>
+<tr class="row-even"><td>USER-PHONON</td>
<td>phonon dynamical matrix</td>
<td>Ling-Ti Kong (Shanghai Jiao Tong U)</td>
<td><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></td>
<td>USER/phonon</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-even"><td>USER-QMMM</td>
+<tr class="row-odd"><td>USER-QMMM</td>
<td>QM/MM coupling</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></td>
<td>USER/qmmm</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/qmmm</td>
</tr>
-<tr class="row-odd"><td>USER-QTB</td>
+<tr class="row-even"><td>USER-QTB</td>
<td>quantum nuclear effects</td>
<td>Yuan Shen (Stanford)</td>
<td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td>
<td>qtb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-even"><td>USER-QUIP</td>
+<tr class="row-odd"><td>USER-QUIP</td>
<td>QUIP/libatoms interface</td>
<td>Albert Bartok-Partay (U Cambridge)</td>
<td><a class="reference internal" href="pair_quip.html"><em>pair_style quip</em></a></td>
<td>USER/quip</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/quip</td>
</tr>
-<tr class="row-odd"><td>USER-REAXC</td>
+<tr class="row-even"><td>USER-REAXC</td>
<td>C version of ReaxFF</td>
<td>Metin Aktulga (LBNL)</td>
<td><a class="reference internal" href="pair_reax_c.html"><em>pair_style reaxc</em></a></td>
<td>reax</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
-<tr class="row-even"><td>USER-SMD</td>
+<tr class="row-odd"><td>USER-SMD</td>
<td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/smd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
+<tr class="row-even"><td>USER-SMTBQ</td>
+<td>Second Moment Tight Binding - QEq potential</td>
+<td>Salles & Maras & Politano & Tetot (4)</td>
+<td><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></td>
+<td>USER/smtbq</td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+</tr>
<tr class="row-odd"><td>USER-SPH</td>
<td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/sph</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-TALLY</td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
<td>USER/tally</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
responible for creating and maintaining the package.</p>
<p>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).</p>
<p>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).</p>
<p>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).</p>
+<p>(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
+Olivier Politano, and Robert Tetot (LAAS-CNRS, France).</p>
<p>If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
library from.</p>
<p>The “Doc page” column links to either a portion of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. <a class="reference internal" href="Section_start.html#start-3-3"><span>Section start</span></a> of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.</p>
<p>Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-user-package
make machine
or
Make.py -p package -a machine
</pre></div>
</div>
<p>To un-install the package and re-build LAMMPS without it:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-user-package
make machine
or
Make.py -p ^package -a machine
</pre></div>
</div>
<p>“Package” is the name of the package (in this case without the user
prefix) in lower-case letters, e.g. drude or phonon, and “machine” is
the build target, e.g. mpi or serial.</p>
</div>
<div class="section" id="user-atc-package">
<h2>4.14. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements a “fix atc” command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.</p>
<p>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.</p>
<p>There are example scripts for using this package in examples/USER/atc.</p>
<p>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-awpmd-package">
<h2>4.15. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.</p>
<p>See the doc page for the pair_style awpmd/cut command to get started.</p>
<p>There are example scripts for using this package in examples/USER/awpmd.</p>
<p>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cg-cmm-package">
<h2>4.16. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements 3 commands which can be used in a LAMMPS input
script:</p>
<ul class="simple">
<li>pair_style lj/sdk</li>
<li>pair_style lj/sdk/coul/long</li>
<li>angle_style sdk</li>
</ul>
<p>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.</p>
<p>See the doc pages for these commands for details.</p>
<p>There are example scripts for using this package in
examples/USER/cg-cmm.</p>
<p>This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.</p>
<p>The current version of this package should be considered beta
quality. The CG potentials work correctly for “normal” situations, but
have not been testing with all kinds of potential parameters and
simulation systems.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-colvars-package">
<h2>4.17. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements the “fix colvars” command which can be
used in a LAMMPS input script.</p>
<p>This fix allows to use “collective variables” to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:</p>
<ul class="simple">
<li>A portable collective variable module library written and maintained</li>
<li>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and</li>
<li>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in</li>
<li>the directory lib/colvars and needs to be compiled first. The colvars</li>
<li>fix and an interface layer, exchanges information between LAMMPS and</li>
<li>the collective variable module.</li>
</ul>
<p>See the doc page of <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> for more details.</p>
<p>There are example scripts for using this package in
examples/USER/colvars</p>
<p>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cuda-package">
<h2>4.18. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>There are example scripts for using this package in
examples/USER/cuda.</p>
<p>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-diffraction-package">
<h2>4.19. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></li>
<li><a class="reference internal" href="compute_saed.html"><em>compute saed</em></a></li>
<li><a class="reference internal" href="fix_saed_vtk.html"><em>fix saed/vtk</em></a></li>
</ul>
<p>The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-drude-package">
<h2>4.20. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="tutorial_drude.html"><em>Drude tutorial</em></a></li>
<li><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a></li>
<li><a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></li>
<li><a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a></li>
<li><a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform/...</em></a></li>
<li><a class="reference internal" href="pair_thole.html"><em>pair thole</em></a></li>
</ul>
<p>There are auxiliary tools for using this package in tools/drude.</p>
<p>The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-eff-package">
<h2>4.21. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.</p>
<p>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.</p>
<p>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.</p>
<p>See the doc page for the pair_style eff/cut command to get started.</p>
<p>There are example scripts for using this package in
examples/USER/eff.</p>
<p>There are auxiliary tools for using this package in tools/eff.</p>
<p>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-fep-package">
<h2>4.22. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a></li>
<li><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></li>
<li><a class="reference internal" href="pair_lj_soft.html"><em>soft pair styles</em></a></li>
</ul>
<p>The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-h5md-package">
<h2>4.23. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command for
performing a dump of atom properties in HDF5 format. <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5 files</a> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The <code class="xref doc docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command gives a
citation to a paper describing the format.</p>
<p>The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>). Contact him
directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-intel-package">
<h2>4.24. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-lb-package">
<h2>4.25. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.</p>
<p>See this doc page and its related commands to get started:</p>
<p><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></p>
<p>The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
+<div class="section" id="user-mgpt-package">
+<h2>4.26. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h2>
+<p>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).</p>
+<p>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 <em>mgpt</em> pair style in this package calculates forces
+and energies using an optimized matrix-MGPT algorithm due to Tomas
+Oppelstrup at LLNL.</p>
+<p>See this doc page to get started:</p>
+<p><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></p>
+<p>The persons who created the USER-MGPT package are Tomas Oppelstrup
+(<a class="reference external" href="mailto:oppelstrup2%40llnl.gov">oppelstrup2<span>@</span>llnl<span>.</span>gov</a>) and John Moriarty (<a class="reference external" href="mailto:moriarty2%40llnl.gov">moriarty2<span>@</span>llnl<span>.</span>gov</a>)
+Contact them directly if you have any questions.</p>
+</div>
+<hr class="docutils" />
<div class="section" id="user-misc-package">
-<h2>4.26. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.27. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
<p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
<p>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:</p>
<p><a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands</span></a></p>
<p>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.</p>
<p>The list of features and author of each is given in the
src/USER-MISC/README file.</p>
<p>You should contact the author directly if you have specific questions
about the feature or its coding.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-molfile-package">
-<h2>4.27. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.28. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.</p>
<p>The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.</p>
<p>See this doc page to get started:</p>
<p><span class="xref std std-ref">dump molfile</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-omp-package">
-<h2>4.28. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.29. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-phonon-package">
-<h2>4.29. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.30. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></p>
<p>The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qmmm-package">
-<h2>4.30. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.31. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
<p>The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></p>
<p>as well as the lib/qmmm/README file.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qtb-package">
-<h2>4.31. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.32. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.</p>
<p>See these two doc pages to get started:</p>
<p><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>.</p>
<p><a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.</p>
<p>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-reaxc-package">
-<h2>4.32. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.33. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.</p>
<p>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.</p>
<p>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.</p>
<p>For technical details about this implemention of ReaxFF, see
this paper:</p>
<p>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).</p>
<p>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.</p>
<p>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-smd-package">
-<h2>4.33. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.34. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
<li>Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.</li>
<li>Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.</li>
<li>Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.</li>
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</li>
</ul>
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
</div>
+<hr class="docutils" />
+<div class="section" id="user-smtbq-package">
+<h2>4.35. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h2>
+<p>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
+potential for the description of ionocovalent bonds in oxides.</p>
+<p>There are example scripts for using this package in
+examples/USER/smtbq.</p>
+<p>See this doc page to get started:</p>
+<p><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></p>
+<p>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: <a class="reference external" href="mailto:lammps%40u-bourgogne.fr">lammps<span>@</span>u-bourgogne<span>.</span>fr</a>, <a class="reference external" href="mailto:nsalles%40laas.fr">nsalles<span>@</span>laas<span>.</span>fr</a>. Contact
+them directly if you have any questions.</p>
+</div>
+<hr class="docutils" />
<div class="section" id="user-sph-package">
-<h2>4.34. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.36. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state</li>
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
<li>Density continuity or density summation to propagate the density field</li>
<li>Commands to set internal energy and density of particles from the
input script</li>
<li>Output commands to access internal energy and density for dumping and
thermo output</li>
</ul>
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/sph.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
</div>
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\ No newline at end of file
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index cfc879fb2..f56fdbce0 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -1,803 +1,857 @@
"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
REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
XTC, dumps in XTC format, -, "dump"_dump.html, -, -
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
More details on
multiple authors are give below.
(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. "Section
start"_Section_start.html#start_3_3 of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.
make yes-package
make machine
or
Make.py -p package -a machine :pre
To un-install the package and re-build LAMMPS without it:
make no-package
make machine
or
Make.py -p ^package -a machine :pre
"Package" is the name of the package in lower-case letters,
e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
serial.
:line
:line
Build instructions for COMPRESS package :h4
:line
Build instructions for GPU package :h4
:line
Build instructions for KIM package :h4
:line
Build instructions for KOKKOS package :h4
:line
Build instructions for KSPACE package :h4
:line
Build instructions for MEAM package :h4
:line
Build instructions for POEMS package :h4
:line
Build instructions for PYTHON package :h4
:line
Build instructions for REAX package :h4
:line
Build instructions for VORONOI package :h4
:line
Build instructions for XTC package :h4
:line
:line
4.2 User packages :h4,link(pkg_2)
The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
+USER-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).
+
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-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.
diff --git a/doc/_images/pair_mgpt.jpg b/doc/_images/pair_mgpt.jpg
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diff --git a/doc/_images/pair_vashishta.jpg b/doc/_images/pair_vashishta.jpg
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diff --git a/doc/_images/polymorphic3.jpg b/doc/_images/polymorphic3.jpg
new file mode 100644
index 000000000..ba748e63c
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diff --git a/doc/doc2/Eqs/pair_mgpt.jpg b/doc/doc2/Eqs/pair_mgpt.jpg
new file mode 100644
index 000000000..2bede7f90
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diff --git a/doc/doc2/Eqs/pair_mgpt.tex b/doc/doc2/Eqs/pair_mgpt.tex
new file mode 100644
index 000000000..9c314df91
--- /dev/null
+++ b/doc/doc2/Eqs/pair_mgpt.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
+ + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
+ + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
+ + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_smtbq1.jpg b/doc/doc2/Eqs/pair_smtbq1.jpg
new file mode 100644
index 000000000..6bfb07b77
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diff --git a/doc/doc2/Eqs/pair_smtbq1.tex b/doc/doc2/Eqs/pair_smtbq1.tex
new file mode 100755
index 000000000..21ae0e9a4
--- /dev/null
+++ b/doc/doc2/Eqs/pair_smtbq1.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{tot} & = & E_{ES} + E_{OO} + E_{MO} \\
+E_{ES} & = & \sum_i{\Big[ \chi_{i}^{0}Q_i + \frac{1}{2}J_{i}^{0}Q_{i}^{2} +
+ \frac{1}{2} \sum_{j\neq i}{ J_{ij}(r_{ij})f_{cut}^{R_{coul}}(r_{ij})Q_i Q_j } \Big] } \\
+E_{OO} & = & \sum_{i,j}^{i,j = O}{\Bigg[Cexp( -\frac{r_{ij}}{\rho} ) - Df_{cut}^{r_1^{OO}r_2^{OO}}(r_{ij}) exp(Br_{ij})\Bigg]} \\
+E_{MO} & = & \sum_i{E_{cov}^{i} + \sum_{j\neq i}{ Af_{cut}^{r_{c1}r_{c2}}(r_{ij})exp\Big[-p(\frac{r_{ij}}{r_0} -1) \Big] } } \\
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_smtbq2.jpg b/doc/doc2/Eqs/pair_smtbq2.jpg
new file mode 100644
index 000000000..0e2024878
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diff --git a/doc/doc2/Eqs/pair_smtbq2.tex b/doc/doc2/Eqs/pair_smtbq2.tex
new file mode 100755
index 000000000..8524c2586
--- /dev/null
+++ b/doc/doc2/Eqs/pair_smtbq2.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{cov}^{i(i=M,O)} & = & - \Bigg\{\eta_i(\mu \xi^{0})^2 f_{cut}^{r_{c1}r_{c2}}(r_{ij})
+\Bigg( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \Bigg)
+\delta Q_i \Big( 2\frac{n_0}{\eta_i} - \delta Q_i \Big) \Bigg\}^{1/2} \\
+\delta Q_i & = & | Q_i^{F} | - | Q_i |
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_smtbq3.jpg b/doc/doc2/Eqs/pair_smtbq3.jpg
new file mode 100644
index 000000000..1d6045916
Binary files /dev/null and b/doc/doc2/Eqs/pair_smtbq3.jpg differ
diff --git a/doc/doc2/Eqs/pair_smtbq3.tex b/doc/doc2/Eqs/pair_smtbq3.tex
new file mode 100755
index 000000000..5bc6e465d
--- /dev/null
+++ b/doc/doc2/Eqs/pair_smtbq3.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\xi^0 & = & \frac{\xi_O}{m} = \frac{\xi_C}{n} \\
+\frac{\beta_O}{\sqrt{m}} & = & \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}\\
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_vashishta.jpg b/doc/doc2/Eqs/pair_vashishta.jpg
new file mode 100644
index 000000000..ca5f118a8
Binary files /dev/null and b/doc/doc2/Eqs/pair_vashishta.jpg differ
diff --git a/doc/doc2/Eqs/pair_vashishta.tex b/doc/doc2/Eqs/pair_vashishta.tex
new file mode 100644
index 000000000..b65056a25
--- /dev/null
+++ b/doc/doc2/Eqs/pair_vashishta.tex
@@ -0,0 +1,22 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ U & = & \sum_i^N \sum_{j > i}^N U_{ij}^{(2)} (r_{ij}) +
+ \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N
+ U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk})
+ \\
+ U_{ij}^{(2)} (r) & = & \frac{H_{ij}}{r^{\eta_{ij}}}
+ + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij})
+ - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij})
+ - \frac{W_{ij}}{r^6}, r < r_{c,{ij}}
+ \\
+ U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = & B_{ijk}
+ \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2}
+ {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\
+& & \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right)
+ \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic1.tex b/doc/doc2/Eqs/polymorphic1.tex
new file mode 100644
index 000000000..b4b925ccf
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E=\frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic2.tex b/doc/doc2/Eqs/polymorphic2.tex
new file mode 100644
index 000000000..80b1c9382
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic2.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+X_{ij}=\sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right)
+\label{X_eq2}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic3.tex b/doc/doc2/Eqs/polymorphic3.tex
new file mode 100644
index 000000000..71db8d81b
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic3.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\Delta r_{jik}=r_{ij}-\xi_{IJ}\cdot r_{ik}
+\label{Dr_eq3}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic4.tex b/doc/doc2/Eqs/polymorphic4.tex
new file mode 100644
index 000000000..b792df82a
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic4.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\left\{\begin{array}{l}
+\eta_{ij}=\delta_{ij},\xi_{IJ}=0 \\
+U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+F_{IJ}\left(X\right)=-X \\
+P_{IJ}\left(\Delta r\right)=1 \\
+W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic5.tex b/doc/doc2/Eqs/polymorphic5.tex
new file mode 100644
index 000000000..a5451b98d
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic5.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\left\{\begin{array}{l}
+\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\
+U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
+V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
+F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\
+P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\
+W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\
+G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right]
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic6.tex b/doc/doc2/Eqs/polymorphic6.tex
new file mode 100644
index 000000000..c8f9f2f25
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic6.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+f_{c,IJ}=\left\{\begin{array}{lr}
+1, & r\leq r_{s,IJ} \\
+\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}<r<r_{c,IJ} \\
+0, & r \geq r_{c,IJ} \\
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic7.tex b/doc/doc2/Eqs/polymorphic7.tex
new file mode 100644
index 000000000..80e991440
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic7.tex
@@ -0,0 +1,25 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\left\{\begin{array}{l}
+\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\
+U_{IJ}\left(r\right)=\left\{\begin{array}{lr}
+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right), & r\leq r_{s,1,IJ} \\
+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)\cdot f_{c,1,IJ}\left(r\right), & r_{s,1,IJ}<r<r_{c,1,IJ} \\
+0, & r\ge r_{c,1,IJ}
+\end{array}\right. \\
+V_{IJ}\left(r\right)=\left\{\begin{array}{lr}
+B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right), & r\le r_{s,1,IJ} \\
+B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot & \\ ~~~~~~ f_{c,IJ}\left(r\right)\cdot \left[1-f_{c,1,IJ}\left(r\right)\right], & r_{s,1,IJ}<r<r_{c,1,IJ} \\
+B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot & \\ ~~~~~~ f_{c,IJ}\left(r\right) & r \ge r_{c,1,IJ}
+\end{array}\right. \\
+F_{IJ}\left(X\right)=\left[1+\left(\beta_{IJ}\cdot X\right)^{n_{IJ}}\right]^{-\frac{1}{2n_{IJ}}} \\
+P_{IJ}\left(\Delta r\right)=exp\left(\lambda_{3,IK}\cdot \Delta r^3\right) \\
+W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\
+G_{JIK}\left(\theta\right)=1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic8.tex b/doc/doc2/Eqs/polymorphic8.tex
new file mode 100644
index 000000000..7d2c872df
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic8.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+f_{c,1,IJ}=\left\{\begin{array}{lr}
+1, & r\leq r_{s,1,IJ} \\
+\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,1,IJ}\right)}{r_{c,1,IJ}-r_{s,1,IJ}}\right], & r_{s,1,IJ}<r<r_{c,1,IJ} \\
+0, & r \geq r_{c,1,IJ} \\
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/polymorphic9.tex b/doc/doc2/Eqs/polymorphic9.tex
new file mode 100644
index 000000000..3d62b12ec
--- /dev/null
+++ b/doc/doc2/Eqs/polymorphic9.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\left\{\begin{array}{l}
+\eta_{ij}=1-\delta_{ij},\xi_{IJ}=0 \\
+U_{IJ}\left(r\right)=\phi_{IJ}\left(r\right) \\
+V_{IJ}\left(r\right)=1 \\
+F_{II}\left(X\right)=-2F_I\left(X\right) \\
+P_{IJ}\left(\Delta r\right)=1 \\
+W_{IJ}\left(r\right)=f_{K}\left(r\right) \\
+G_{JIK}\left(\theta\right)=1
+\end{array}\right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html
index f76689504..0ddcdedea 100644
--- a/doc/doc2/Manual.html.html
+++ b/doc/doc2/Manual.html.html
@@ -1,318 +1,318 @@
<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Oct 2015 version">
+<META NAME="docnumber" CONTENT="23 Oct 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<!-- END_HTML_ONLY -->
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
-<CENTER><H4>22 Oct 2015 version
+<CENTER><H4>23 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
</P>
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
</HTML>
diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html
index 411376f9d..4e3e097fb 100644
--- a/doc/doc2/Section_commands.html
+++ b/doc/doc2/Section_commands.html
@@ -1,668 +1,668 @@
<HTML>
<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A>
</CENTER>
<HR>
<H3>3. Commands
</H3>
<P>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<HR>
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
</P>
<P>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
</P>
<P>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
</P>
<PRE>timestep 0.5
run 100
run 100
</PRE>
<P>does something different than this sequence:
</P>
<PRE>run 100
timestep 0.5
run 100
</PRE>
<P>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
</P>
<P>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
</P>
<P>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<A HREF = "read_data.html">read_data</A> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <A HREF = "processors.html">processors</A> and
<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
</P>
<P>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
</P>
<P>Here is how each line in the input script is parsed by LAMMPS:
</P>
<P>(1) If the last printable character on the line is a "&" character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the "&" character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using "&" characters.
</P>
<P>(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
</P>
<P>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
</P>
<P>If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
"x".
</P>
<P>How the variable is converted to a text string depends on what style
of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
</P>
<P>As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an <A HREF = "variable.html">equal-style variable</A>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
</P>
<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</PRE>
<P>can be replaced by
</P>
<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</PRE>
<P>so that you do not have to define (or discard) a temporary variable X.
</P>
<P>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
</P>
<PRE>variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
</PRE>
<P>Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
<A HREF = "variable.html">equal-style variable</A>.
</P>
<P>See the <A HREF = "variable.html">variable</A> command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
</P>
<P>(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
</P>
<P>(5) The first word is the command name. All successive words in the
line are arguments.
</P>
<P>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the "&" character is used, as described above. When
the lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
</P>
<PRE>print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
</PRE>
<P>In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
</P>
<P>See the <A HREF = "dump_modify.html">dump modify format</A>, <A HREF = "print.html">print</A>,
<A HREF = "if.html">if</A>, and <A HREF = "python.html">python</A> commands for examples.
</P>
<P>A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
</P>
<P>IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
WWW Site</A>.
</P>
<P>A LAMMPS input script typically has 4 parts:
</P>
<OL><LI>Initialization
<LI>Atom definition
<LI>Settings
<LI>Run a simulation
</OL>
<P>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
</P>
<P>(1) Initialization
</P>
<P>Set parameters that need to be defined before atoms are created or
read-in from a file.
</P>
<P>The relevant commands are <A HREF = "units.html">units</A>,
<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
</P>
<P>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_style.html">improper_style</A>.
</P>
<P>(2) Atom definition
</P>
<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
duplicated to make a larger simulation using the
<A HREF = "replicate.html">replicate</A> command.
</P>
<P>(3) Settings
</P>
<P>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
</P>
<P>Force field coefficients are set by these commands (they can also be
set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
<A HREF = "special_bonds.html">special_bonds</A>.
</P>
<P>Various simulation parameters are set by these commands:
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
</P>
<P>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
</P>
<P>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</P>
<P>(4) Run a simulation
</P>
<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
command. Energy minimization (molecular statics) is performed using
the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
(replica-exchange) simulation can be run using the
<A HREF = "temper.html">temper</A> command.
</P>
<HR>
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<P>Initialization:
</P>
<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
</P>
<P>Atom definition:
</P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
</P>
<P>Force fields:
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "improper_style.html">improper_style</A>,
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P>Settings:
</P>
<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
</P>
<P>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</A>
</P>
<P>Output:
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
</P>
<P>Actions:
</P>
<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
</P>
<P>Miscellaneous:
</P>
<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
</P>
<HR>
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "comm_modify.html">comm_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "comm_style.html">comm_style</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_bonds.html">create_bonds</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "info.html">info</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "python.html">python</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "timer.html">timer</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<P>These are additional commands in USER packages, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Fix styles
</H4>
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the <A HREF = "Section_accelerate.html">appropriate accelerated package</A>.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce (c)</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_atom_swap.html">atom/swap</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce (c)</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_chunk.html">ave/chunk</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo/weight</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform (k)</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d (c)</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze (c)</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity (co)</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin (k)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (ko)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (cko)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (cko)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_qeq.html">qeq/dynamic</A></TD><TD ><A HREF = "fix_qeq.html">qeq/point</A></TD><TD ><A HREF = "fix_qeq.html">qeq/shielded</A></TD><TD ><A HREF = "fix_qeq.html">qeq/slater</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csld</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_tfmc.html">tfmc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect (k)</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are additional fix styles in USER packages, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_correlate_long.html">ave/correlate/long</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD><TD ><A HREF = "fix_smd_integrate_tlsph.html">smd/integrate/tlsph</A></TD><TD ><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate/ulsph</A></TD><TD ><A HREF = "fix_smd_move_triangulated_surface.html">smd/move/triangulated/surface</A></TD><TD ><A HREF = "fix_smd_setvel.html">smd/setvel</A></TD><TD ><A HREF = "fix_smd_tlsph_reference_configuration.html">smd/tlsph/reference/configuration</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Compute styles
</H4>
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_angmom_chunk.html">angmom/chunk</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_chunk_atom.html">chunk/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna_atom.html">sna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sna_atom.html">snad/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (ck)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
</TD></TR></TABLE></DIV>
<P>These are additional compute styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_tally.html">force/tally</A></TD><TD ><A HREF = "compute_tally.html">heat/flux/tally</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_tally.html">pe/tally</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_contact_radius.html">smd/contact/radius</A></TD><TD ><A HREF = "compute_smd_damage.html">smd/damage</A></TD><TD ><A HREF = "compute_smd_hourglass_error.html">smd/hourglass/error</A></TD><TD ><A HREF = "compute_smd_internal_energy.html">smd/internal/energy</A></TD><TD ><A HREF = "compute_smd_plastic_strain.html">smd/plastic/strain</A></TD><TD ><A HREF = "compute_smd_plastic_strain_rate.html">smd/plastic/strain/rate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_rho.html">smd/rho</A></TD><TD ><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph/defgrad</A></TD><TD ><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph/dt</A></TD><TD ><A HREF = "compute_smd_tlsph_num_neighs.html">smd/tlsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_tlsph_shape.html">smd/tlsph/shape</A></TD><TD ><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph/strain</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_tlsph_stress.html">smd/tlsph/stress</A></TD><TD ><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle/mesh/vertices</A></TD><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain_rate.html">smd/ulsph/strain/rate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_stress.html">smd/ulsph/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_tally.html">stress/tally</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Pair_style potentials
</H4>
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cs</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cs</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/cs</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/streitz</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (ko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgkot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy (cgkot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgkot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgiko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (cko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_cubic.html">lj/cubic (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cs</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff (cgko)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_vashishta.html">vashishta (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
</TD></TR></TABLE></DIV>
<P>These are additional pair styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd (o)</A></TD><TD ><A HREF = "pair_edip.html">edip (o)</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
+<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_mgpt.html">mgpt</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_smtbq.html">smtbq</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Bond_style potentials
</H4>
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_none.html">none</A></TD><TD ><A HREF = "bond_hybrid.html">hybrid</A></TD><TD ><A HREF = "bond_class2.html">class2 (o)</A></TD><TD ><A HREF = "bond_fene.html">fene (ko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_fene_expand.html">fene/expand (o)</A></TD><TD ><A HREF = "bond_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "bond_morse.html">morse (o)</A></TD><TD ><A HREF = "bond_nonlinear.html">nonlinear (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_quartic.html">quartic (o)</A></TD><TD ><A HREF = "bond_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional bond styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift (o)</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Angle_style potentials
</H4>
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_none.html">none</A></TD><TD ><A HREF = "angle_hybrid.html">hybrid</A></TD><TD ><A HREF = "angle_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "angle_class2.html">class2 (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_cosine.html">cosine (o)</A></TD><TD ><A HREF = "angle_cosine_delta.html">cosine/delta (o)</A></TD><TD ><A HREF = "angle_cosine_periodic.html">cosine/periodic (o)</A></TD><TD ><A HREF = "angle_cosine_squared.html">cosine/squared (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "angle_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional angle styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_cosine_shift.html">cosine/shift (o)</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "angle_dipole.html">dipole (o)</A></TD><TD ><A HREF = "angle_fourier.html">fourier (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_fourier_simple.html">fourier/simple (o)</A></TD><TD ><A HREF = "angle_quartic.html">quartic (o)</A></TD><TD ><A HREF = "angle_sdk.html">sdk</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Dihedral_style potentials
</H4>
<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_none.html">none</A></TD><TD ><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD ><A HREF = "dihedral_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "dihedral_class2.html">class2 (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "dihedral_helix.html">helix (o)</A></TD><TD ><A HREF = "dihedral_multi_harmonic.html">multi/harmonic (o)</A></TD><TD ><A HREF = "dihedral_opls.html">opls (ko)</A>
</TD></TR></TABLE></DIV>
<P>These are additional dihedral styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier (o)</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic (o)</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Improper_style potentials
</H4>
<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_none.html">none</A></TD><TD ><A HREF = "improper_hybrid.html">hybrid</A></TD><TD ><A HREF = "improper_class2.html">class2 (o)</A></TD><TD ><A HREF = "improper_cvff.html">cvff (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "improper_umbrella.html">umbrella (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional improper styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq (o)</A></TD><TD ><A HREF = "improper_fourier.html">fourier (o)</A></TD><TD ><A HREF = "improper_ring.html">ring (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Kspace solvers
</H4>
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald (o)</A></TD><TD ><A HREF = "kspace_style.html">ewald/disp</A></TD><TD ><A HREF = "kspace_style.html">msm (o)</A></TD><TD ><A HREF = "kspace_style.html">msm/cg (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm (cgo)</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg (o)</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/tip4p (o)</A>
</TD></TR></TABLE></DIV>
</HTML>
diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html
index 16186a05d..56f1eb343 100644
--- a/doc/doc2/Section_packages.html
+++ b/doc/doc2/Section_packages.html
@@ -1,821 +1,875 @@
<HTML>
<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
Section</A>
</CENTER>
<HR>
<H3>4. Packages
</H3>
<P>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.
</P>
4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
4.2 <A HREF = "#pkg_2">User packages</A> <BR>
<P>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
</P>
<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.
</P>
<P>Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
packages include commands derived from commands in other packages. If
the other package is not installed, the derived command from the new
package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE pacakge and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
</P>
<P>The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sections below give a few more
details, including instructions for building LAMMPS with the package,
either via the make command or the Make.py tool described in <A HREF = "Section_start.html#start_4">Section
2.4</A>.
</P>
<HR>
<HR>
<H4><A NAME = "pkg_1"></A>4.1 Standard packages
</H4>
<P>The current list of standard packages is as follows.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COMPRESS</TD><TD > I/O compression</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump.html">dump */gz</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
<TR ALIGN="center"><TD >PYTHON</TD><TD > embed Python code in an input script</TD><TD > -</TD><TD > <A HREF = "python.html">python</A></TD><TD > python</TD><TD > lib/python</TD></TR>
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</TD></TR>
<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
More details on
multiple authors are give below.
</P>
<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
</P>
<P>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
</P>
<P>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
</P>
<P>(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section
start</A> of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
</P>
<P>Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.
</P>
<PRE>make yes-package
make machine
or
Make.py -p package -a machine
</PRE>
<P>To un-install the package and re-build LAMMPS without it:
</P>
<PRE>make no-package
make machine
or
Make.py -p ^package -a machine
</PRE>
<P>"Package" is the name of the package in lower-case letters,
e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
serial.
</P>
<HR>
<HR>
<H4>Build instructions for COMPRESS package
</H4>
<HR>
<H4>Build instructions for GPU package
</H4>
<HR>
<H4>Build instructions for KIM package
</H4>
<HR>
<H4>Build instructions for KOKKOS package
</H4>
<HR>
<H4>Build instructions for KSPACE package
</H4>
<HR>
<H4>Build instructions for MEAM package
</H4>
<HR>
<H4>Build instructions for POEMS package
</H4>
<HR>
<H4>Build instructions for PYTHON package
</H4>
<HR>
<H4>Build instructions for REAX package
</H4>
<HR>
<H4>Build instructions for VORONOI package
</H4>
<HR>
<H4>Build instructions for XTC package
</H4>
<HR>
<HR>
<H4><A NAME = "pkg_2"></A>4.2 User packages
</H4>
<P>The current list of user-contributed packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > lib/h5md</TD></TR>
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-MGPT</TD><TD > fast MGPT multi-ion potentials</TD><TD > Tomas Oppelstrup & John Moriarty (LLNL)</TD><TD > <A HREF = "pair_mgpt.html">pair_style mgpt</A></TD><TD > USER/mgpt</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QUIP/libatoms interface</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "pair_quip.html">pair_style quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SMD</TD><TD > smoothed Mach dynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/smd</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-SMTBQ</TD><TD > Second Moment Tight Binding - QEq potential</TD><TD > Salles & Maras & Politano & Tetot (4)</TD><TD > <A HREF = "pair_smtbq.html">pair_style smtbq</A></TD><TD > USER/smtbq</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-TALLY</TD><TD > Pairwise tallied computes</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "compute_tally.html">compute <...>/tally</A></TD><TD > USER/tally</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
</P>
<P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
</P>
<P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
</P>
+<P>(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
+Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
+</P>
<P>If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
library from.
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.
</P>
<P>Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.
</P>
<PRE>make yes-user-package
make machine
or
Make.py -p package -a machine
</PRE>
<P>To un-install the package and re-build LAMMPS without it:
</P>
<PRE>make no-user-package
make machine
or
Make.py -p ^package -a machine
</PRE>
<P>"Package" is the name of the package (in this case without the user
prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
the build target, e.g. mpi or serial.
</P>
<HR>
<HR>
<H4>USER-ATC package
</H4>
<P>This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
</P>
<P>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
</P>
<P>There are example scripts for using this package in examples/USER/atc.
</P>
<P>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
</P>
<HR>
<H4>USER-AWPMD package
</H4>
<P>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
</P>
<P>See the doc page for the pair_style awpmd/cut command to get started.
</P>
<P>There are example scripts for using this package in examples/USER/awpmd.
</P>
<P>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-CG-CMM package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script:
</P>
<UL><LI>pair_style lj/sdk
<LI>pair_style lj/sdk/coul/long
<LI>angle_style sdk
</UL>
<P>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>There are example scripts for using this package in
examples/USER/cg-cmm.
</P>
<P>This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.
</P>
<P>The current version of this package should be considered beta
quality. The CG potentials work correctly for "normal" situations, but
have not been testing with all kinds of potential parameters and
simulation systems.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-COLVARS package
</H4>
<P>This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
</P>
<P>This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
</P>
<UL><LI>A portable collective variable module library written and maintained
<LI>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
<LI>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
<LI>the directory lib/colvars and needs to be compiled first. The colvars
<LI>fix and an interface layer, exchanges information between LAMMPS and
<LI>the collective variable module.
</UL>
<P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details.
</P>
<P>There are example scripts for using this package in
examples/USER/colvars
</P>
<P>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-CUDA package
</H4>
<P>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_7">Section_accelerate</A>
</P>
<P>There are example scripts for using this package in
examples/USER/cuda.
</P>
<P>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-DIFFRACTION package
</H4>
<P>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "compute_xrd.html">compute xrd</A>
<LI><A HREF = "compute_saed.html">compute saed</A>
<LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A>
</UL>
<P>The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
</P>
<HR>
<H4>USER-DRUDE package
</H4>
<P>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "tutorial_drude.html">Drude tutorial</A>
<LI><A HREF = "fix_drude.html">fix drude</A>
<LI><A HREF = "compute_temp_drude.html">compute temp/drude</A>
<LI><A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
<LI><A HREF = "fix_drude_transform.html">fix drude/transform/...</A>
<LI><A HREF = "pair_thole.html">pair thole</A>
</UL>
<P>There are auxiliary tools for using this package in tools/drude.
</P>
<P>The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.
</P>
<HR>
<H4>USER-EFF package
</H4>
<P>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
</P>
<P>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
</P>
<P>See the doc page for the pair_style eff/cut command to get started.
</P>
<P>There are example scripts for using this package in
examples/USER/eff.
</P>
<P>There are auxiliary tools for using this package in tools/eff.
</P>
<P>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-FEP package
</H4>
<P>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>
<LI><A HREF = "compute_fep.html">compute fep</A>
<LI><A HREF = "pair_lj_soft.html">soft pair styles</A>
</UL>
<P>The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
</P>
<HR>
<H4>USER-H5MD package
</H4>
<P>This package contains a <A HREF = "dump_h5md.html">dump h5md</A> command for
performing a dump of atom properties in HDF5 format. <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5
files</A> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The <A HREF = "doc/dump_h5md.html">dump h5md</A> command gives a
citation to a paper describing the format.
</P>
<P>The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
directly if you have questions.
</P>
<HR>
<H4>USER-INTEL package
</H4>
<P>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A>
</P>
<P>The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-LB package
</H4>
<P>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
</P>
<P>See this doc page and its related commands to get started:
</P>
<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>
</P>
<P>The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.
</P>
<HR>
+<H4>USER-MGPT package
+</H4>
+<P>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).
+</P>
+<P>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 <I>mgpt</I> pair style in this package calculates forces
+and energies using an optimized matrix-MGPT algorithm due to Tomas
+Oppelstrup at LLNL.
+</P>
+<P>See this doc page to get started:
+</P>
+<P><A HREF = "pair_mgpt.html">pair_style mgpt</A>
+</P>
+<P>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.
+</P>
+<HR>
+
<H4>USER-MISC package
</H4>
<P>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
</P>
<P>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
</P>
<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
</P>
<P>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
</P>
<P>The list of features and author of each is given in the
src/USER-MISC/README file.
</P>
<P>You should contact the author directly if you have specific questions
about the feature or its coding.
</P>
<HR>
<H4>USER-MOLFILE package
</H4>
<P>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
</P>
<P>The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "dump_molfile.html#acc_5">dump molfile</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-OMP package
</H4>
<P>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_5">Section_accelerate</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-PHONON package
</H4>
<P>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "fix_phonon.html">fix phonon</A>
</P>
<P>The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
</P>
<HR>
<H4>USER-QMMM package
</H4>
<P>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> package.
</P>
<P>The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "fix_qmmm.html">fix qmmm</A>
</P>
<P>as well as the lib/qmmm/README file.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-QTB package
</H4>
<P>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.
</P>
<P>See these two doc pages to get started:
</P>
<P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>.
</P>
<P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.
</P>
<P>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-REAXC package
</H4>
<P>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
</P>
<P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
</P>
<P>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
</P>
<P>For technical details about this implemention of ReaxFF, see
this paper:
</P>
<P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
</P>
<P>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
</P>
<P>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
</P>
<HR>
<H4>USER-SMD package
</H4>
<P>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
</P>
<P>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
</P>
<P>* Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.
</P>
<P>* Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.
</P>
<P>* Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.
</P>
<P>* Rigid boundary conditions (walls) can be loaded as surface geometries
from *.STL files.
</P>
<P>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/smd.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
+<HR>
+
+<H4>USER-SMTBQ package
+</H4>
+<P>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
+potential for the description of ionocovalent bonds in oxides.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/smtbq.
+</P>
+<P>See this doc page to get started:
+</P>
+<P><A HREF = "pair_smtbq.html">pair_style smtbq</A>
+</P>
+<P>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.
+</P>
+<HR>
+
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
</P>
<P>* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
</P>
<P>* Plain or Monaghans XSPH integration of the equations of motion
</P>
<P>* Density continuity or density summation to propagate the density field
</P>
<P>* Commands to set internal energy and density of particles from the
input script
</P>
<P>* Output commands to access internal energy and density for dumping and
thermo output
</P>
<P>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/sph.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
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<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#J"><strong>J</strong></a>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#Q"><strong>Q</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_coeff.html#index-0">angle_coeff</a>
</dt>
<dt><a href="angle_style.html#index-0">angle_style</a>
</dt>
<dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
</dt>
<dt><a href="angle_class2.html#index-0">angle_style class2</a>
</dt>
<dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
</dt>
<dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
</dt>
<dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
</dt>
<dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
</dt>
<dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
</dt>
<dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
</dt>
<dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
</dt>
<dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
</dt>
<dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
</dt>
<dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
</dt>
<dt><a href="angle_none.html#index-0">angle_style none</a>
</dt>
<dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
</dt>
<dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
</dt>
<dt><a href="angle_table.html#index-0">angle_style table</a>
</dt>
<dt><a href="atom_modify.html#index-0">atom_modify</a>
</dt>
<dt><a href="atom_style.html#index-0">atom_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="balance.html#index-0">balance</a>
</dt>
<dt><a href="bond_coeff.html#index-0">bond_coeff</a>
</dt>
<dt><a href="bond_style.html#index-0">bond_style</a>
</dt>
<dt><a href="bond_class2.html#index-0">bond_style class2</a>
</dt>
<dt><a href="bond_fene.html#index-0">bond_style fene</a>
</dt>
<dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
</dt>
<dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
</dt>
<dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
</dt>
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt>
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt>
<dt><a href="bond_none.html#index-0">bond_style none</a>
</dt>
<dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
</dt>
<dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
</dt>
<dt><a href="bond_table.html#index-0">bond_style table</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a>
</dt>
<dt><a href="box.html#index-0">box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="change_box.html#index-0">change_box</a>
</dt>
<dt><a href="clear.html#index-0">clear</a>
</dt>
<dt><a href="comm_modify.html#index-0">comm_modify</a>
</dt>
<dt><a href="comm_style.html#index-0">comm_style</a>
</dt>
<dt><a href="compute.html#index-0">compute</a>
</dt>
<dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
</dt>
<dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
</dt>
<dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
</dt>
<dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
</dt>
<dt><a href="compute_body_local.html#index-0">compute body/local</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt>
<dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
</dt>
<dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
</dt>
<dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
</dt>
<dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
</dt>
<dt><a href="compute_com.html#index-0">compute com</a>
</dt>
<dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
</dt>
<dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
</dt>
<dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
</dt>
<dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
</dt>
<dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
</dt>
<dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
<dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
</dt>
<dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
</dt>
<dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
</dt>
<dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
</dt>
<dt><a href="compute_fep.html#index-0">compute fep</a>
</dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt>
<dt><a href="compute_gyration.html#index-0">compute gyration</a>
</dt>
<dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
</dt>
<dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt>
<dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
</dt>
<dt><a href="compute_ke.html#index-0">compute ke</a>
</dt>
<dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
</dt>
<dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
</dt>
<dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
</dt>
<dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
</dt>
<dt><a href="compute_meso_e_atom.html#index-0">compute meso_e/atom</a>
</dt>
<dt><a href="compute_meso_rho_atom.html#index-0">compute meso_rho/atom</a>
</dt>
<dt><a href="compute_meso_t_atom.html#index-0">compute meso_t/atom</a>
</dt>
<dt><a href="compute_msd.html#index-0">compute msd</a>
</dt>
<dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
</dt>
<dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
</dt>
<dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt>
<dt><a href="compute_property_local.html#index-0">compute property/local</a>
</dt>
<dt><a href="compute_rdf.html#index-0">compute rdf</a>
</dt>
<dt><a href="compute_reduce.html#index-0">compute reduce</a>
</dt>
<dt><a href="compute_saed.html#index-0">compute saed</a>
</dt>
<dt><a href="compute_slice.html#index-0">compute slice</a>
</dt>
<dt><a href="compute_smd_contact_radius.html#index-0">compute smd/contact_radius</a>
</dt>
<dt><a href="compute_smd_damage.html#index-0">compute smd/damage</a>
</dt>
<dt><a href="compute_smd_hourglass_error.html#index-0">compute smd/hourglass_error</a>
</dt>
<dt><a href="compute_smd_internal_energy.html#index-0">compute smd/internal_energy</a>
</dt>
<dt><a href="compute_smd_plastic_strain.html#index-0">compute smd/plastic_strain</a>
</dt>
<dt><a href="compute_smd_plastic_strain_rate.html#index-0">compute smd/plastic_strain_rate</a>
</dt>
<dt><a href="compute_smd_rho.html#index-0">compute smd/rho</a>
</dt>
<dt><a href="compute_smd_tlsph_defgrad.html#index-0">compute smd/tlsph_defgrad</a>
</dt>
<dt><a href="compute_smd_tlsph_dt.html#index-0">compute smd/tlsph_dt</a>
</dt>
<dt><a href="compute_smd_tlsph_num_neighs.html#index-0">compute smd/tlsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_tlsph_shape.html#index-0">compute smd/tlsph_shape</a>
</dt>
<dt><a href="compute_smd_tlsph_strain.html#index-0">compute smd/tlsph_strain</a>
</dt>
<dt><a href="compute_smd_tlsph_strain_rate.html#index-0">compute smd/tlsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_tlsph_stress.html#index-0">compute smd/tlsph_stress</a>
</dt>
<dt><a href="compute_smd_ulsph_num_neighs.html#index-0">compute smd/ulsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_ulsph_strain.html#index-0">compute smd/ulsph_strain</a>
</dt>
<dt><a href="compute_smd_ulsph_strain_rate.html#index-0">compute smd/ulsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_ulsph_stress.html#index-0">compute smd/ulsph_stress</a>
</dt>
<dt><a href="compute_smd_vol.html#index-0">compute smd/vol</a>
</dt>
<dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
</dt>
<dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
</dt>
<dt><a href="compute_temp.html#index-0">compute temp</a>
</dt>
<dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
</dt>
<dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
</dt>
<dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
</dt>
<dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
</dt>
<dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
</dt>
<dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
</dt>
<dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
</dt>
<dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
</dt>
<dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
</dt>
<dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
</dt>
<dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
</dt>
<dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
</dt>
<dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
</dt>
<dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
</dt>
<dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
</dt>
<dt><a href="compute_ti.html#index-0">compute ti</a>
</dt>
<dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
</dt>
<dt><a href="compute_vacf.html#index-0">compute vacf</a>
</dt>
<dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
</dt>
<dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
</dt>
<dt><a href="compute_xrd.html#index-0">compute xrd</a>
</dt>
<dt><a href="compute_modify.html#index-0">compute_modify</a>
</dt>
<dt><a href="create_atoms.html#index-0">create_atoms</a>
</dt>
<dt><a href="create_bonds.html#index-0">create_bonds</a>
</dt>
<dt><a href="create_box.html#index-0">create_box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="delete_atoms.html#index-0">delete_atoms</a>
</dt>
<dt><a href="delete_bonds.html#index-0">delete_bonds</a>
</dt>
<dt><a href="dielectric.html#index-0">dielectric</a>
</dt>
<dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
</dt>
<dt><a href="dihedral_style.html#index-0">dihedral_style</a>
</dt>
<dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
</dt>
<dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
</dt>
<dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
</dt>
<dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
</dt>
<dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
</dt>
<dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
</dt>
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
</dt>
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
</dt>
<dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
</dt>
<dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
</dt>
<dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
</dt>
<dt><a href="dimension.html#index-0">dimension</a>
</dt>
<dt><a href="displace_atoms.html#index-0">displace_atoms</a>
</dt>
<dt><a href="dump.html#index-0">dump</a>
</dt>
<dt><a href="dump_h5md.html#index-0">dump h5md</a>
</dt>
<dt><a href="dump_image.html#index-0">dump image</a>
</dt>
<dt><a href="dump_molfile.html#index-0">dump molfile</a>
</dt>
<dt><a href="dump_modify.html#index-0">dump_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="echo.html#index-0">echo</a>
</dt>
</dl></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix.html#index-0">fix</a>
</dt>
<dt><a href="fix_adapt.html#index-0">fix adapt</a>
</dt>
<dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
</dt>
<dt><a href="fix_addforce.html#index-0">fix addforce</a>
</dt>
<dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
</dt>
<dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
</dt>
<dt><a href="fix_atc.html#index-0">fix atc</a>
</dt>
<dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
</dt>
<dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
</dt>
<dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
</dt>
<dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
</dt>
<dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
</dt>
<dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
</dt>
<dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
</dt>
<dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
</dt>
<dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
</dt>
<dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
</dt>
<dt><a href="fix_balance.html#index-0">fix balance</a>
</dt>
<dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
</dt>
<dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
</dt>
<dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
</dt>
<dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
</dt>
<dt><a href="fix_colvars.html#index-0">fix colvars</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>
<dt><a href="fix_deposit.html#index-0">fix deposit</a>
</dt>
<dt><a href="fix_drag.html#index-0">fix drag</a>
</dt>
<dt><a href="fix_drude.html#index-0">fix drude</a>
</dt>
<dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
</dt>
<dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
</dt>
<dt><a href="fix_efield.html#index-0">fix efield</a>
</dt>
<dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
<dt><a href="fix_external.html#index-0">fix external</a>
</dt>
<dt><a href="fix_freeze.html#index-0">fix freeze</a>
</dt>
<dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
</dt>
<dt><a href="fix_gld.html#index-0">fix gld</a>
</dt>
<dt><a href="fix_gle.html#index-0">fix gle</a>
</dt>
<dt><a href="fix_gravity.html#index-0">fix gravity</a>
</dt>
<dt><a href="fix_heat.html#index-0">fix heat</a>
</dt>
<dt><a href="fix_imd.html#index-0">fix imd</a>
</dt>
<dt><a href="fix_indent.html#index-0">fix indent</a>
</dt>
<dt><a href="fix_ipi.html#index-0">fix ipi</a>
</dt>
<dt><a href="fix_langevin.html#index-0">fix langevin</a>
</dt>
<dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
</dt>
<dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
</dt>
<dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
</dt>
<dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
</dt>
<dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
</dt>
<dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
</dt>
<dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
</dt>
<dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
<dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
</dt>
<dt><a href="fix_momentum.html#index-0">fix momentum</a>
</dt>
<dt><a href="fix_move.html#index-0">fix move</a>
</dt>
<dt><a href="fix_msst.html#index-0">fix msst</a>
</dt>
<dt><a href="fix_neb.html#index-0">fix neb</a>
</dt>
<dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
</dt>
<dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
</dt>
<dt><a href="fix_nphug.html#index-0">fix nphug</a>
</dt>
<dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
</dt>
<dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>
<dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
</dt>
<dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
</dt>
<dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
</dt>
<dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
</dt>
<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
<dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
</dt>
<dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
</dt>
<dt><a href="fix_nh.html#index-0">fix nvt</a>
</dt>
<dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
</dt>
<dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
</dt>
<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
</dt>
<dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
</dt>
<dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
</dt>
<dt><a href="fix_oneway.html#index-0">fix oneway</a>
</dt>
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
</dt>
<dt><a href="fix_phonon.html#index-0">fix phonon</a>
</dt>
<dt><a href="fix_pimd.html#index-0">fix pimd</a>
</dt>
<dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
</dt>
<dt><a href="fix_pour.html#index-0">fix pour</a>
</dt>
<dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
</dt>
<dt><a href="fix_print.html#index-0">fix print</a>
</dt>
<dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
</dt>
<dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
</dt>
<dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
</dt>
<dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
</dt>
<dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
</dt>
<dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
</dt>
<dt><a href="fix_qtb.html#index-0">fix qtb</a>
</dt>
<dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
</dt>
<dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
</dt>
<dt><a href="fix_recenter.html#index-0">fix recenter</a>
</dt>
<dt><a href="fix_restrain.html#index-0">fix restrain</a>
</dt>
<dt><a href="fix_rigid.html#index-0">fix rigid</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
<dt><a href="fix_setforce.html#index-0">fix setforce</a>
</dt>
<dt><a href="fix_shake.html#index-0">fix shake</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
<dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
</dt>
<dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
</dt>
<dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
</dt>
<dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
</dt>
<dt><a href="fix_smd_setvel.html#index-0">fix smd/setvel</a>
</dt>
<dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
</dt>
<dt><a href="fix_spring.html#index-0">fix spring</a>
</dt>
<dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
</dt>
<dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
</dt>
<dt><a href="fix_srd.html#index-0">fix srd</a>
</dt>
<dt><a href="fix_store_force.html#index-0">fix store/force</a>
</dt>
<dt><a href="fix_store_state.html#index-0">fix store/state</a>
</dt>
<dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
</dt>
<dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
</dt>
<dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
</dt>
<dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
</dt>
<dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
</dt>
<dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
</dt>
<dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
</dt>
<dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
</dt>
<dt><a href="fix_tmd.html#index-0">fix tmd</a>
</dt>
<dt><a href="fix_ttm.html#index-0">fix ttm</a>
</dt>
<dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
</dt>
<dt><a href="fix_vector.html#index-0">fix vector</a>
</dt>
<dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
</dt>
<dt><a href="fix_viscous.html#index-0">fix viscous</a>
</dt>
<dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
</dt>
<dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
</dt>
<dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
</dt>
<dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
</dt>
<dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
</dt>
<dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
</dt>
<dt><a href="fix_modify.html#index-0">fix_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group.html#index-0">group</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group2ndx.html#index-0">group2ndx</a>
</dt>
</dl></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="if.html#index-0">if</a>
</dt>
<dt><a href="improper_coeff.html#index-0">improper_coeff</a>
</dt>
<dt><a href="improper_style.html#index-0">improper_style</a>
</dt>
<dt><a href="improper_class2.html#index-0">improper_style class2</a>
</dt>
<dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
</dt>
<dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
</dt>
<dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
</dt>
<dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
</dt>
<dt><a href="improper_none.html#index-0">improper_style none</a>
</dt>
<dt><a href="improper_ring.html#index-0">improper_style ring</a>
</dt>
<dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
</dt>
<dt><a href="include.html#index-0">include</a>
</dt>
<dt><a href="info.html#index-0">info</a>
</dt>
</dl></td>
</tr></table>
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="jump.html#index-0">jump</a>
</dt>
</dl></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_modify.html#index-0">kspace_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_style.html#index-0">kspace_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="label.html#index-0">label</a>
</dt>
<dt><a href="lattice.html#index-0">lattice</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="log.html#index-0">log</a>
</dt>
</dl></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="mass.html#index-0">mass</a>
</dt>
<dt><a href="min_modify.html#index-0">min_modify</a>
</dt>
<dt><a href="min_style.html#index-0">min_style</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="minimize.html#index-0">minimize</a>
</dt>
<dt><a href="molecule.html#index-0">molecule</a>
</dt>
</dl></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="neb.html#index-0">neb</a>
</dt>
<dt><a href="neigh_modify.html#index-0">neigh_modify</a>
</dt>
<dt><a href="neighbor.html#index-0">neighbor</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="newton.html#index-0">newton</a>
</dt>
<dt><a href="next.html#index-0">next</a>
</dt>
</dl></td>
</tr></table>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="package.html#index-0">package</a>
</dt>
<dt><a href="pair_coeff.html#index-0">pair_coeff</a>
</dt>
<dt><a href="pair_modify.html#index-0">pair_modify</a>
</dt>
<dt><a href="pair_style.html#index-0">pair_style</a>
</dt>
<dt><a href="pair_adp.html#index-0">pair_style adp</a>
</dt>
<dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
</dt>
<dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
</dt>
<dt><a href="pair_beck.html#index-0">pair_style beck</a>
</dt>
<dt><a href="pair_body.html#index-0">pair_style body</a>
</dt>
<dt><a href="pair_bop.html#index-0">pair_style bop</a>
</dt>
<dt><a href="pair_born.html#index-0">pair_style born</a>
</dt>
<dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
</dt>
<dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
</dt>
<dt><a href="pair_buck.html#index-0">pair_style buck</a>
</dt>
<dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
</dt>
<dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
</dt>
<dt><a href="pair_comb.html#index-0">pair_style comb</a>
</dt>
<dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
</dt>
<dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
</dt>
<dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
</dt>
<dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
</dt>
<dt><a href="pair_eam.html#index-0">pair_style eam</a>
</dt>
<dt><a href="pair_edip.html#index-0">pair_style edip</a>
</dt>
<dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
</dt>
<dt><a href="pair_eim.html#index-0">pair_style eim</a>
</dt>
<dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
</dt>
<dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
</dt>
<dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
</dt>
<dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
</dt>
<dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
</dt>
<dt><a href="pair_kim.html#index-0">pair_style kim</a>
</dt>
<dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
</dt>
<dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
</dt>
<dt><a href="pair_list.html#index-0">pair_style list</a>
</dt>
<dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
</dt>
<dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
</dt>
<dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
</dt>
<dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
</dt>
<dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
</dt>
<dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
</dt>
<dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
</dt>
<dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
</dt>
<dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
</dt>
<dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
</dt>
<dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
</dt>
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
<dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
</dt>
<dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
</dt>
<dt><a href="pair_meam.html#index-0">pair_style meam</a>
</dt>
+ <dt><a href="pair_mgpt.html#index-0">pair_style mgpt</a>
+ </dt>
+
+
<dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
</dt>
<dt><a href="pair_morse.html#index-0">pair_style morse</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>
<dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
</dt>
<dt><a href="pair_none.html#index-0">pair_style none</a>
</dt>
<dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
</dt>
<dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
</dt>
<dt><a href="pair_quip.html#index-0">pair_style quip</a>
</dt>
<dt><a href="pair_reax.html#index-0">pair_style reax</a>
</dt>
<dt><a href="pair_reax_c.html#index-0">pair_style reax/c</a>
</dt>
<dt><a href="pair_resquared.html#index-0">pair_style resquared</a>
</dt>
<dt><a href="pair_smd_hertz.html#index-0">pair_style smd/hertz</a>
</dt>
<dt><a href="pair_smd_tlsph.html#index-0">pair_style smd/tlsph</a>
</dt>
<dt><a href="pair_smd_triangulated_surface.html#index-0">pair_style smd/tri_surface</a>
</dt>
<dt><a href="pair_smd_ulsph.html#index-0">pair_style smd/ulsph</a>
</dt>
+ <dt><a href="pair_smtbq.html#index-0">pair_style smtbq</a>
+ </dt>
+
+
<dt><a href="pair_snap.html#index-0">pair_style snap</a>
</dt>
<dt><a href="pair_soft.html#index-0">pair_style soft</a>
</dt>
<dt><a href="pair_sph_heatconduction.html#index-0">pair_style sph/heatconduction</a>
</dt>
<dt><a href="pair_sph_idealgas.html#index-0">pair_style sph/idealgas</a>
</dt>
<dt><a href="pair_sph_lj.html#index-0">pair_style sph/lj</a>
</dt>
<dt><a href="pair_sph_rhosum.html#index-0">pair_style sph/rhosum</a>
</dt>
<dt><a href="pair_sph_taitwater.html#index-0">pair_style sph/taitwater</a>
</dt>
<dt><a href="pair_sph_taitwater_morris.html#index-0">pair_style sph/taitwater/morris</a>
</dt>
<dt><a href="pair_srp.html#index-0">pair_style srp</a>
</dt>
<dt><a href="pair_sw.html#index-0">pair_style sw</a>
</dt>
<dt><a href="pair_table.html#index-0">pair_style table</a>
</dt>
<dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
</dt>
<dt><a href="pair_tersoff_mod.html#index-0">pair_style tersoff/mod</a>
</dt>
<dt><a href="pair_tersoff_zbl.html#index-0">pair_style tersoff/zbl</a>
</dt>
<dt><a href="pair_thole.html#index-0">pair_style thole</a>
</dt>
<dt><a href="pair_tri_lj.html#index-0">pair_style tri/lj</a>
</dt>
<dt><a href="pair_vashishta.html#index-0">pair_style vashishta</a>
</dt>
<dt><a href="pair_yukawa.html#index-0">pair_style yukawa</a>
</dt>
<dt><a href="pair_yukawa_colloid.html#index-0">pair_style yukawa/colloid</a>
</dt>
<dt><a href="pair_zbl.html#index-0">pair_style zbl</a>
</dt>
<dt><a href="pair_write.html#index-0">pair_write</a>
</dt>
<dt><a href="partition.html#index-0">partition</a>
</dt>
<dt><a href="prd.html#index-0">prd</a>
</dt>
<dt><a href="print.html#index-0">print</a>
</dt>
<dt><a href="processors.html#index-0">processors</a>
</dt>
<dt><a href="python.html#index-0">python</a>
</dt>
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</dt>
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</dt>
<dt><a href="region.html#index-0">region</a>
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</dt>
</dl></td>
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<dt><a href="rerun.html#index-0">rerun</a>
</dt>
<dt><a href="reset_timestep.html#index-0">reset_timestep</a>
</dt>
<dt><a href="restart.html#index-0">restart</a>
</dt>
<dt><a href="run.html#index-0">run</a>
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<dt><a href="run_style.html#index-0">run_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="S">S</h2>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="set.html#index-0">set</a>
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<dt><a href="special_bonds.html#index-0">special_bonds</a>
</dt>
<dt><a href="suffix.html#index-0">suffix</a>
</dt>
</dl></td>
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<h2 id="T">T</h2>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="tad.html#index-0">tad</a>
</dt>
<dt><a href="temper.html#index-0">temper</a>
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<dt><a href="thermo.html#index-0">thermo</a>
</dt>
<dt><a href="thermo_modify.html#index-0">thermo_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="thermo_style.html#index-0">thermo_style</a>
</dt>
<dt><a href="timer.html#index-0">timer</a>
</dt>
<dt><a href="timestep.html#index-0">timestep</a>
</dt>
</dl></td>
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<h2 id="U">U</h2>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="uncompute.html#index-0">uncompute</a>
</dt>
<dt><a href="undump.html#index-0">undump</a>
</dt>
</dl></td>
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<dt><a href="unfix.html#index-0">unfix</a>
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<dt><a href="units.html#index-0">units</a>
</dt>
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<h2 id="V">V</h2>
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<dt><a href="variable.html#index-0">variable</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="velocity.html#index-0">velocity</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="write_data.html#index-0">write_data</a>
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\ No newline at end of file
diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html
new file mode 100644
index 000000000..9d6e62def
--- /dev/null
+++ b/doc/doc2/pair_mgpt.html
@@ -0,0 +1,229 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style mgpt command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style mgpt
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
+(<A HREF = "#Moriarty1">Moriarty1</A>) provides a first-principles approach to
+multi-ion interatomic potentials in d-band transition metals, with a
+volume-dependent, real-space total-energy functional for the N-ion
+elemental bulk material in the form
+</P>
+<CENTER><IMG SRC = "Eqs/pair_mgpt.jpg">
+</CENTER>
+<P>where the prime on each summation sign indicates the exclusion of all
+self-interaction terms from the summation. The leading volume term
+E_vol as well as the two-ion central-force pair potential v_2 and the
+three- and four-ion angular-force potentials, v_3 and v_4, depend
+explicitly on the atomic volume Omega, but are structure independent
+and transferable to all bulk ion configurations, either ordered or
+disordered, and with of without the presence of point and line
+defects. The simplified model GPT or MGPT (<A HREF = "#Moriarty2">Moriarty2</A>,
+<A HREF = "#Moriarty3">Moriarty3</A>), which retains the form of E_tot and permits
+more efficient large-scale atomistic simulations, derives from the GPT
+through a series of systematic approximations applied to E_vol and the
+potentials v_n that are valid for mid-period transition metals with
+nearly half-filled d bands.
+</P>
+<P>Both analytic (<A HREF = "#Moriarty2">Moriarty2</A>) and matrix
+(<A HREF = "#Moriarty3">Moriarty3</A>) representations of MGPT have been developed.
+In the more general matrix representation, which can also be applied
+to f-band actinide metals and permits both canonical and non-canonical
+d/f bands, 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. Fast matrix-MGPT
+algorithms have been developed independently by Glosli
+(<A HREF = "#Glosi">Glosli</A>, <A HREF = "#Moriarty3">Moriarty3</A>) and by Oppelstrup
+(<A HREF = "#Oppelstrup">Oppelstrup</A>)
+</P>
+<P>The <I>mgpt</I> pair style calculates forces, energies, and the total
+energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
+Input potential and control data are entered through the
+<A HREF = "pair_coeff.html">pair_coeff</A> command. Each material treated requires
+input parmin and potin potential files, as shown in the above
+examples, as well as specification by the user of the initial atomic
+volume Omega through pair_coeff. At the beginning of a time step in
+any simulation, the total volume of the simulation cell V should
+always be equal to Omega*N, where N is the number of metal ions
+present, taking into account the presence of any vacancies and/or
+interstitials in the case of a solid. In a constant-volume
+simulation, which is the normal mode of operation for the <I>mgpt</I> pair
+style, Omega, V and N all remain constant throughout the simulation
+and thus are equal to their initial values. In a constant-stress
+simulation, the cell volume V will change (slowly) as the simulation
+proceeds. After each time step, the atomic volume should be updated
+by the code as Omega = V/N. In addition, the volume term E_vol and
+the potentials v_2, v_3 and v_4 have to be removed at the end of the
+time step, and then respecified at the new value of Omega. In all
+smulations, Omega must remain within the defined volume range for
+E_vol and the potentials for the given material.
+</P>
+<P>The default option volpress yes in the <A HREF = "pair_coeff.html">pair_coeff</A>
+command includes all volume derivatives of E_tot required to calculate
+the stress tensor and pressure correctly. The option volpress no
+disregards the pressure contribution resulting from the volume term
+E_vol, and can be used for testing and analysis purposes. The
+additional optional variable nbody controls the specific terms in
+E_tot that are calculated. The default option and the normal option
+for mid-period transition and actinide metals is nbody 1234 for which
+all four terms in E_tot are retained. The option nbody 12, for
+example, retains only the volume term and the two-ion pair potential
+term and can be used for GPT series-end transition metals that can be
+well described without v_3 and v_4. The nbody option can also be used
+to test or analyze the contribution of any of the four terms in E_tot
+to a given calculated property.
+</P>
+<P>The <I>mgpt</I> pair style makes extensive use of matrix algebra and
+includes optimized kernels for the BlueGene/Q architecture and the
+Intel/AMD (x86) architectures. When compiled with the appropriate
+compiler and compiler switches (-msse3 on x86, and using the IBM XL
+compiler on BG/Q), these optimized routines are used automatically.
+For BG/Q machines, building with the default Makefile for that
+architecture (e.g., "make bgq") should enable the optimized algebra
+routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
+(build with "make mpi_fastmgpt") enables the fast algebra routines.
+The user will be informed in the output files of the matrix kernels in
+use. To further improve speed, on x86 the option precision single can
+be added to the <A HREF = "pair_coeff.html">pair_coeff</A> command line, which
+improves speed (up to a factor of two) at the cost of doing matrix
+calculations with 7 digit precision instead of the default 16. For
+consistency the default option can be specified explicitly by the
+option precision double.
+</P>
+<P>All remaining potential and control data are contained with the parmin
+and potin files, including cutoffs, atomic mass, and other basic MGPT
+variables. Specific MGPT potential data for the transition metals
+tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
+and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
+directory. The stored files are, respectively, Ta4.mgpt.parmin,
+Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
+Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
+V6.1.mgpt.potin . Useful corresponding informational "README" files
+on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
+potentials directory. These latter files indicate the volume mesh and
+range for each potential and give appropriate references for the
+potentials. It is expected that MGPT potentials for additional
+materials will be added over time.
+</P>
+<P>Useful example MGPT scripts are given in the examples/USER/mgpt
+directory. These scripts show the necessary steps to perform
+constant-volume calculations and simulations. It is strongly
+recommended that the user work through and understand these examples
+before proceeding to more complex simulations.
+</P>
+<P>IMPORTANT NOTE: For good performance, LAMMPS should be built with the
+compiler flags "-O3 -msse3 -funroll-loops" when including this pair
+style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example
+machine Makefile with these options included as part of a standard MPI
+build. Note that as-is it will build with whatever low-level compiler
+(g++, icc, etc) is the default for your MPI installation.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table tail correction, restart</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-MGPT package and is only enabled
+if LAMMPS is built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The MGPT potentials require the <A HREF = "newton.html">newtion</A> setting to be
+"on" for pair style interactions.
+</P>
+<P>The stored parmin and potin potential files provided with LAMMPS in
+the "potentials" directory are written in Rydberg atomic units, with
+energies in Rydbergs and distances in Bohr radii. The <I>mgpt</I> pair
+style converts Rydbergs to Hartrees to make the potential files
+compatible with LAMMPS electron <A HREF = "units.html">units</A>.
+</P>
+<P>The form of E_tot used in the <I>mgpt</I> pair style is only appropriate
+for elemental bulk solids and liquids. This includes solids with
+point and extended defects such as vacancies, interstitials, grain
+boundaries and dislocations. Alloys and free surfaces, however,
+require significant modifications, which are not included in the
+<I>mgpt</I> pair style. Likewise, the <I>hybrid</I> pair style is not allowed,
+where MGPT would be used for some atoms but not for others.
+</P>
+<P>Electron-thermal effects are not included in the standard MGPT
+potentials provided in the "potentials" directory, where the
+potentials have been constructed at zero electron temperature.
+Physically, electron-thermal effects may be important in 3d (e.g., V)
+and 4d (e.g., Mo) transition metals at high temperatures near melt and
+above. It is expected that temperature-dependent MGPT potentials for
+such cases will be added over time.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The options defaults for the <A HREF = "pair_coeff.html">pair_coeff</A> command are
+volpress yes, nbody 1234, and precision double.
+</P>
+<HR>
+
+<A NAME = "Moriarty1"></A>
+
+<P><B>(Moriarty1)</B> Moriarty, Physical Review B, 38, 3199 (1988).
+</P>
+<A NAME = "Moriarty2"></A>
+
+<P><B>(Moriarty2)</B> Moriarty, Physical Review B, 42, 1609 (1990).
+Moriarty, Physical Review B 49, 12431 (1994).
+</P>
+<A NAME = "Moriarty3"></A>
+
+<P><B>(Moriarty3)</B> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
+Journal of Materials Research, 21, 563 (2006).
+</P>
+<A NAME = "Glosli"></A>
+
+<P><B>(Glosli)</B> Glosli, unpublished, 2005.
+Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
+Series, 46, 254 (2006).
+</P>
+<A NAME = "Oppelstrup"></A>
+
+<P><B>(Oppelstrup)</B> Oppelstrup, unpublished, 2015.
+Oppelstrup and Moriarty, to be published.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_smtbq.html b/doc/doc2/pair_smtbq.html
new file mode 100644
index 000000000..3efce316c
--- /dev/null
+++ b/doc/doc2/pair_smtbq.html
@@ -0,0 +1,272 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style smtbq command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style smtbq
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This pair stylecomputes a variable charge SMTB-Q (Second-Moment
+tight-Binding QEq) potential as described in <A HREF = "#SMTB-Q_1">SMTB-Q_1</A> and
+<A HREF = "#SMTB-Q_2">SMTB-Q_2</A>. Briefly, the energy of metallic-oxygen systems
+is given by three contributions:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_smtbq1.jpg">
+</CENTER>
+<P>where <I>E<sub>tot</sub></I> is the total potential energy of the system,
+<I>E<sub>ES</sub></I> is the electrostatic part of the total energy,
+<I>E<sub>OO</sub></I> is the interaction between oxygens and
+<I>E<sub>MO</sub></I> is a short-range interaction between metal and oxygen
+atoms. This interactions depend on interatomic distance
+<I>r<sub>ij</sub></I> and/or the charge <I>Q<sub>i</sub></I> of atoms
+<I>i</I>. Cut-off function enables smooth convergence to zero interaction.
+</P>
+<P>The parameters appearing in the upper expressions are set in the
+ffield.SMTBQ.Syst file where Syst corresponds to the selected system
+(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>,
+Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command
+is used with the SMTBQ styles which provides the path to the potential
+file with parameters for needed elements. These are mapped to LAMMPS
+atom types by specifying additional arguments after the potential
+filename in the pair_coeff command. Note that atom type 1 must always
+correspond to oxygen atoms. As an example, to simulate a TiO2 system,
+atom type 1 has to be oxygen and atom type 2 Ti. The following
+pair_coeff command should then be used:
+</P>
+<PRE>pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+</PRE>
+The electrostatic part of the energy consists of two components
+
+<P>self-energy of atom <I>i</I> in the form of a second order charge dependent
+polynomial and a long-range Coulombic electrostatic interaction. The
+latter uses the wolf summation method described in <A HREF = "#Wolf">Wolf</A>,
+spherically truncated at a longer cutoff, <I>R<sub>coul</sub></I>. The
+charge of each ion is modeled by an orbital Slater which depends on
+the principal quantum number (<I>n</I>) of the outer orbital shared by the
+ion.
+</P>
+<P>Interaction between oxygen, <I>E<sub>OO</sub></I>, consists of two parts,
+an attractive and a repulsive part. The attractive part is effective
+only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive
+contribution was optimized to study surfaces reconstruction
+(e.g. <A HREF = "#SMTB-Q_2">SMTB-Q_2</A> in TiO<sub>2</sub>) and is not necessary
+for oxide bulk modeling. The repulsive part is the Pauli interaction
+between the electron clouds of oxygen. The Pauli repulsion and the
+coulombic electrostatic interaction have same cut off value. In the
+ffield.SMTBQ.Syst, the keyword <I>'buck'</I> allows to consider only the
+repulsive O-O interactions. The keyword <I>'buckPlusAttr'</I> allows to
+consider the repulsive and the attractive O-O interactions.
+</P>
+<P>The short-range interaction between metal-oxygen, <I>E<sub>MO</sub></I> is
+based on the second moment approximation of the density of states with
+a N-body potential for the band energy term,
+<I>E<sup>i</sup><sub>cov</sub></I>, and a Born-Mayer type repulsive terms
+as indicated by the keyword <I>'second_moment'</I> in the
+ffield.SMTBQ.Syst. The energy band term is given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_smtbq2.jpg">
+</CENTER>
+<P>where <I>η<sub>i</sub></I> is the stoichiometry of atom <I>i</I>,
+<I>δQ<sub>i</sub></I> is the charge delocalization of atom <I>i</I>,
+compared to its formal charge
+<I>Q<sup>F</sup><sub>i</sub></I>. n<sub>0</sub>, the number of hybridized
+orbitals, is calculated with to the atomic orbitals shared
+<I>d<sub>i</sub></I> and the stoichiometry
+<I>η<sub>i</sub></I>. <I>r<sub>c1</sub></I> and <I>r<sub>c2</sub></I> are the two
+cutoff radius around the fourth neighbors in the cutoff function.
+</P>
+<P>In the formalism used here, <I>ξ<sup>0</sup></I> is the energy
+parameter. <I>ξ<sup>0</sup></I> is in tight-binding approximation the
+hopping integral between the hybridized orbitals of the cation and the
+anion. In the literature we find many ways to write the hopping
+integral depending on whether one takes the point of view of the anion
+or cation. These are equivalent vision. The correspondence between the
+two visions is explained in appendix A of the article in the
+SrTiO<sub>3</sub> <A HREF = "#SMTB-Q_3">SMTB-Q_3</A> (parameter <I>β</I> shown in
+this article is in fact the <I>β<sub>O</sub></I>). To summarize the
+relationship between the hopping integral <I>ξ<sup>0</sup></I> and the
+others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following
+relationship:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_smtbq3.jpg">
+</CENTER>
+<P>Thus parameter μ, indicated above, is given by : μ = (√n
++ √m) ⁄ 2
+</P>
+<P>The potential offers the possibility to consider the polarizability of
+the electron clouds of oxygen by changing the slater radius of the
+charge density around the oxygens through the parameters <I>rBB, rB and
+rS</I> in the ffield.SMTBQ.Syst. This change in radius is performed
+according to the method developed by E. Maras
+<A HREF = "#SMTB-Q_2">SMTB-Q_2</A>. This method needs to determine the number of
+nearest neighbors around the oxygen. This calculation is based on
+first (<I>r<sub>1n</sub></I>) and second (<I>r<sub>2n</sub></I>) distances
+neighbors.
+</P>
+<P>The SMTB-Q potential is a variable charge potential. The equilibrium
+charge on each atom is calculated by the electronegativity
+equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for further detail. One
+can adjust the frequency, the maximum number of iterative loop and the
+convergence of the equilibrium charge calculation. To obtain the
+energy conservation in NVE thermodynamic ensemble, we recommend to use
+a convergence parameter in the interval 10<sup>-5</sup> -
+10<sup>-6</sup> eV.
+</P>
+<P>The ffield.SMTBQ.Syst files are provided for few systems. They consist
+of nine parts and the lines beginning with '#' are comments (note that
+the number of comment lines matter). The first sections are on the
+potential parameters and others are on the simulation options and
+might be modified. Keywords are character type and must be enclosed in
+quotation marks ('').
+</P>
+<P>1) Number of different element in the oxide:
+</P>
+<UL><LI>N<sub>elem</sub>= 2 or 3
+<LI>Divided line
+</UL>
+<P>2) Atomic parameters
+</P>
+For the anion (oxygen)
+
+<UL><LI>Name of element (char) and stoichiometry in oxide
+<LI>Formal charge and mass of element
+<LI>Principal quantic number of outer orbital (<I>n</I>), electronegativity (<I>χ<sup>0</sup><sub>i</simulationub></I>) and hardness (<I>J<sup>0</sup><sub>i</sub></I>)
+<LI> Ionic radius parameters : max coordination number (<I>coordBB</I> = 6 by default), bulk coordination number <I>(coordB)</I>, surface coordination number <I>(coordS)</I> and <I>rBB, rB and rS</I> the slater radius for each coordination number. (<b>note : If you don't want to change the slater radius, use three identical radius values</b>)
+<LI>Number of orbital shared by the element in the oxide (<I>d<sub>i</sub></I>)
+<LI>Divided line
+</UL>
+<P>For each cations (metal):
+</P>
+<UL><LI>Name of element (char) and stoichiometry in oxide
+<LI>Formal charge and mass of element
+<LI>Number of electron in outer orbital <I>(ne)</I>, electronegativity (<I>χ<sup>0</sup><sub>i</simulationub></I>), hardness (<I>J<sup>0</sup><sub>i</sub></I>) and <I>r<sub>Salter</sub></I> the slater radius for the cation.
+<LI>Number of orbitals shared by the elements in the oxide (<I>d<sub>i</sub></I>)
+<LI>Divided line
+</UL>
+<P>3) Potential parameters:
+</P>
+<UL><LI>Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
+<LI>Potential parameter: <pre><br/> If type of potential is 'second_moment' : <I>A (eV)</I>, <I>p</I>, <I>ξ<sup>0</sup></I> (eV) and <I>q</I> <br/> <I>r<sub>c1</sub></I> (Å), <I>r<sub>c2</sub></I> (Å) and <I>r<sub>0</sub></I> (Å) <br/> If type of potential is 'buck' : <I>C</I> (eV) and <I>ρ</I> (Å) <br/> If type of potential is 'buckPlusAttr' : <I>C</I> (eV) and <I>ρ</I> (Å) <br/> <I>D</I> (eV), <I>B</I> (Å<sup>-1</sup>), <I>r<sub>1</sub><sup>OO</sup></I> (Å) and <I>r<sub>2</sub><sup>OO</sup></I> (Å) </pre>
+<LI>Divided line
+</UL>
+<P>4) Tables parameters:
+</P>
+<UL><LI>Cutoff radius for the Coulomb interaction (<I>R<sub>coul</sub></I>)
+<LI>Starting radius (<I>r<sub>min</sub></I> = 1,18845 Å) and increments (<I>dr</I> = 0,001 Å) for creating the potential table.
+<LI>Divided line
+</UL>
+<P>5) Rick model parameter:
+</P>
+<UL><LI><I>Nevery</I> : parameter to set the frequency (<I>1/Nevery</I>) of the charge resolution. The charges are evaluated each <I>Nevery</I> time steps.
+<LI>Max number of iterative loop (<I>loopmax</I>) and precision criterion (<I>prec</I>) in eV of the charge resolution
+<LI>Divided line
+</UL>
+<P>6) Coordination parameter:
+</P>
+<UL><LI>First (<I>r<sub>1n</sub></I>) and second (<I>r<sub>2n</sub></I>) neighbor distances in Å
+<LI>Divided line
+</UL>
+<P>7) Charge initialization mode:
+</P>
+<UL><LI>Keyword (<I>QInitMode</I>) and initial oxygen charge (<I>Q<sub>init</sub></I>). If keyword = 'true', all oxygen charges are initially set equal to <I>Q<sub>init</sub></I>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using <A HREF = "#read_data.html">read_data</A> command.
+<LI>Divided line
+</UL>
+8) Mode for the electronegativity equalization (Qeq)
+
+<UL><LI>Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
+<LI>Parameter if necessary
+<LI>Divided line
+</UL>
+9) Verbose
+
+<UL><LI>If you want the code to work in verbose mode or not : 'true' or 'false'
+<LI>If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and <I>N<sub>Energy</sub></I>. This option writes in file every <I>N<sub>Energy</sub></I> time step. If the value is 'false' then <I>N<sub>Energy</sub></I> = 0. The file take into account the possibility to have several QEq group <I>g</I> then it writes: time step, number of atoms in group <I>g</I>, electrostatic part of energy, <I>E<sub>ES</sub></I>, the interaction between oxygen, <I>E<sub>OO</sub></I>, and short range metal-oxygen interaction, <I>E<sub>MO</sub></I>.
+<LI>If you want to print in file 'Electroneg_component.txt' the electronegativity component (<I>∂E<sub>tot</sub> ⁄∂Q<sub>i</sub></I>) or not: 'true' or 'false' and <I>N<sub>Electroneg</sub></I>.This option writes in file every <I>N<sub>Electroneg</sub></I> time step. If the value is 'false' then <I>N<sub>Electroneg</sub></I> = 0. The file consist in atom number <I>i</I>, atom type (1 for oxygen and # higher than 1 for metal), atom position: <I>x</I>, <I>y</I> and <I>z</I>, atomic charge of atom <I>i</I>, electrostatic part of atom <I>i</I> electronegativity, covalent part of atom <I>i</I> electronegativity, the hopping integral of atom <I>i</I> <I>(Zβ<sup>2</sup>)<sub>i<sub></I> and box electronegativity.
+</UL>
+<P>IMPORTANT NOTE: This last option slows down the calculation
+dramatically. Use only with a single processor simulation.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info:</B>
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restriction:</B>
+</P>
+<P>This pair style is part of the USER-SMTBQ package and is only enabled
+if LAMMPS is built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This potential requires using atom type 1 for oxygen and atom type
+higher than 1 for metal atoms.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The SMTB-Q potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal <A HREF = "unit.html">units</A>.
+</P>
+<HR>
+
+<P><B>Citing this work:</B>
+</P>
+<P>Please cite related publication: N. Salles, O. Politano, E. Amzallag
+and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+</P>
+<HR>
+
+<A NAME = "SMTB-Q_1"></A>
+
+<P><B>(SMTB-Q_1)</B> N. Salles, O. Politano, E. Amzallag, R. Tetot,
+Comput. Mater. Sci. 111 (2016) 181-189
+</P>
+<A NAME = "SMTB-Q_2"></A>
+
+<P><B>(SMTB-Q_2)</B> E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
+H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
+</P>
+<A NAME = "SMTB-Q_3"></A>
+
+<P><B>(SMTB-Q_3)</B> R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
+Science 616, 19-8722 28 (2013)
+</P>
+<A NAME = "Wolf"></A>
+
+<P><B>(Wolf)</B> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).
+</P>
+<A NAME = "Rick"></A>
+
+<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).
+</P>
+</HTML>
diff --git a/doc/doc2/temper.html b/doc/doc2/temper.html
index fd5727b88..6523d1303 100644
--- a/doc/doc2/temper.html
+++ b/doc/doc2/temper.html
@@ -1,137 +1,137 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>temper command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>temper N M temp fix-ID seed1 seed2 index
</PRE>
<UL><LI>N = total # of timesteps to run
<LI>M = attempt a tempering swap every this many steps
<LI>temp = initial temperature for this ensemble
<LI>fix-ID = ID of the fix that will control temperature during the run
<LI>seed1 = random # seed used to decide on adjacent temperature to partner with
<LI>seed2 = random # seed for Boltzmann factor in Metropolis swap
<LI>index = which temperature (0 to N-1) I am simulating (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w
</PRE>
<P><B>Description:</B>
</P>
<P>Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_7">Section_start 6</A> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
section</A> of the manual for further
discussion.
</P>
<P>Each replica's temperature is controlled at a different value by a fix
with <I>fix-ID</I> that controls temperature. Possible fix styles are
<A HREF = "fix_nh.html">nvt</A>, <A HREF = "fix_nh.html">temp/berendsen</A>,
<A HREF = "fix_langevin.html">langevin</A> and <A HREF = "fix_temp_rescale.html">temp/rescale</A>.
The desired temperature is specified by <I>temp</I>, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the <A HREF = "variable.html">variable</A>
command for more details. For example:
</P>
<PRE>variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt $t $t 100.0
+fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382
</PRE>
<P>would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.
</P>
<P>As the tempering simulation runs for <I>N</I> timesteps, a temperature swap
between adjacent ensembles will be attempted every <I>M</I> timesteps. If
<I>seed1</I> is 0, then the swap attempts will alternate between odd and
even pairings. If <I>seed1</I> is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
<I>seed2</I> in the random number generator.
</P>
<P>As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the <A HREF = "Section_start.html#start_7">section on command-line
switches</A> for info on how to change these
names.
</P>
<P>The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
</P>
<PRE>Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
...
</PRE>
<P>The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
</P>
<P>The last argument <I>index</I> in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The <I>index</I> value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the <I>N</I> values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:
</P>
<PRE>500000 2 4 0 1 3
</PRE>
<P>then a setting of
</P>
<PRE>variable w world 2 4 0 1 3
</PRE>
<P>would be used to restart the run with a tempering command like the
example above with $w as the last argument.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable</A>, <A HREF = "prd.html">prd</A>, <A HREF = "neb.html">neb</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/genindex.html b/doc/genindex.html
index 36d13dad4..cc20eff0f 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -1,2228 +1,2236 @@
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<title>Index — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#J"><strong>J</strong></a>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#Q"><strong>Q</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_coeff.html#index-0">angle_coeff</a>
</dt>
<dt><a href="angle_style.html#index-0">angle_style</a>
</dt>
<dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
</dt>
<dt><a href="angle_class2.html#index-0">angle_style class2</a>
</dt>
<dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
</dt>
<dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
</dt>
<dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
</dt>
<dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
</dt>
<dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
</dt>
<dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
</dt>
<dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
</dt>
<dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
</dt>
<dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
</dt>
<dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
</dt>
<dt><a href="angle_none.html#index-0">angle_style none</a>
</dt>
<dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
</dt>
<dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
</dt>
<dt><a href="angle_table.html#index-0">angle_style table</a>
</dt>
<dt><a href="atom_modify.html#index-0">atom_modify</a>
</dt>
<dt><a href="atom_style.html#index-0">atom_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="balance.html#index-0">balance</a>
</dt>
<dt><a href="bond_coeff.html#index-0">bond_coeff</a>
</dt>
<dt><a href="bond_style.html#index-0">bond_style</a>
</dt>
<dt><a href="bond_class2.html#index-0">bond_style class2</a>
</dt>
<dt><a href="bond_fene.html#index-0">bond_style fene</a>
</dt>
<dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
</dt>
<dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
</dt>
<dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
</dt>
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt>
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt>
<dt><a href="bond_none.html#index-0">bond_style none</a>
</dt>
<dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
</dt>
<dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
</dt>
<dt><a href="bond_table.html#index-0">bond_style table</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a>
</dt>
<dt><a href="box.html#index-0">box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="change_box.html#index-0">change_box</a>
</dt>
<dt><a href="clear.html#index-0">clear</a>
</dt>
<dt><a href="comm_modify.html#index-0">comm_modify</a>
</dt>
<dt><a href="comm_style.html#index-0">comm_style</a>
</dt>
<dt><a href="compute.html#index-0">compute</a>
</dt>
<dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
</dt>
<dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
</dt>
<dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
</dt>
<dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
</dt>
<dt><a href="compute_body_local.html#index-0">compute body/local</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt>
<dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
</dt>
<dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
</dt>
<dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
</dt>
<dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
</dt>
<dt><a href="compute_com.html#index-0">compute com</a>
</dt>
<dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
</dt>
<dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
</dt>
<dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
</dt>
<dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
</dt>
<dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
</dt>
<dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
<dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
</dt>
<dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
</dt>
<dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
</dt>
<dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
</dt>
<dt><a href="compute_fep.html#index-0">compute fep</a>
</dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt>
<dt><a href="compute_gyration.html#index-0">compute gyration</a>
</dt>
<dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
</dt>
<dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt>
<dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
</dt>
<dt><a href="compute_ke.html#index-0">compute ke</a>
</dt>
<dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
</dt>
<dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
</dt>
<dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
</dt>
<dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
</dt>
<dt><a href="compute_meso_e_atom.html#index-0">compute meso_e/atom</a>
</dt>
<dt><a href="compute_meso_rho_atom.html#index-0">compute meso_rho/atom</a>
</dt>
<dt><a href="compute_meso_t_atom.html#index-0">compute meso_t/atom</a>
</dt>
<dt><a href="compute_msd.html#index-0">compute msd</a>
</dt>
<dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
</dt>
<dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
</dt>
<dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt>
<dt><a href="compute_property_local.html#index-0">compute property/local</a>
</dt>
<dt><a href="compute_rdf.html#index-0">compute rdf</a>
</dt>
<dt><a href="compute_reduce.html#index-0">compute reduce</a>
</dt>
<dt><a href="compute_saed.html#index-0">compute saed</a>
</dt>
<dt><a href="compute_slice.html#index-0">compute slice</a>
</dt>
<dt><a href="compute_smd_contact_radius.html#index-0">compute smd/contact_radius</a>
</dt>
<dt><a href="compute_smd_damage.html#index-0">compute smd/damage</a>
</dt>
<dt><a href="compute_smd_hourglass_error.html#index-0">compute smd/hourglass_error</a>
</dt>
<dt><a href="compute_smd_internal_energy.html#index-0">compute smd/internal_energy</a>
</dt>
<dt><a href="compute_smd_plastic_strain.html#index-0">compute smd/plastic_strain</a>
</dt>
<dt><a href="compute_smd_plastic_strain_rate.html#index-0">compute smd/plastic_strain_rate</a>
</dt>
<dt><a href="compute_smd_rho.html#index-0">compute smd/rho</a>
</dt>
<dt><a href="compute_smd_tlsph_defgrad.html#index-0">compute smd/tlsph_defgrad</a>
</dt>
<dt><a href="compute_smd_tlsph_dt.html#index-0">compute smd/tlsph_dt</a>
</dt>
<dt><a href="compute_smd_tlsph_num_neighs.html#index-0">compute smd/tlsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_tlsph_shape.html#index-0">compute smd/tlsph_shape</a>
</dt>
<dt><a href="compute_smd_tlsph_strain.html#index-0">compute smd/tlsph_strain</a>
</dt>
<dt><a href="compute_smd_tlsph_strain_rate.html#index-0">compute smd/tlsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_tlsph_stress.html#index-0">compute smd/tlsph_stress</a>
</dt>
<dt><a href="compute_smd_ulsph_num_neighs.html#index-0">compute smd/ulsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_ulsph_strain.html#index-0">compute smd/ulsph_strain</a>
</dt>
<dt><a href="compute_smd_ulsph_strain_rate.html#index-0">compute smd/ulsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_ulsph_stress.html#index-0">compute smd/ulsph_stress</a>
</dt>
<dt><a href="compute_smd_vol.html#index-0">compute smd/vol</a>
</dt>
<dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
</dt>
<dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
</dt>
<dt><a href="compute_temp.html#index-0">compute temp</a>
</dt>
<dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
</dt>
<dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
</dt>
<dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
</dt>
<dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
</dt>
<dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
</dt>
<dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
</dt>
<dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
</dt>
<dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
</dt>
<dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
</dt>
<dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
</dt>
<dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
</dt>
<dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
</dt>
<dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
</dt>
<dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
</dt>
<dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
</dt>
<dt><a href="compute_ti.html#index-0">compute ti</a>
</dt>
<dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
</dt>
<dt><a href="compute_vacf.html#index-0">compute vacf</a>
</dt>
<dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
</dt>
<dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
</dt>
<dt><a href="compute_xrd.html#index-0">compute xrd</a>
</dt>
<dt><a href="compute_modify.html#index-0">compute_modify</a>
</dt>
<dt><a href="create_atoms.html#index-0">create_atoms</a>
</dt>
<dt><a href="create_bonds.html#index-0">create_bonds</a>
</dt>
<dt><a href="create_box.html#index-0">create_box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="delete_atoms.html#index-0">delete_atoms</a>
</dt>
<dt><a href="delete_bonds.html#index-0">delete_bonds</a>
</dt>
<dt><a href="dielectric.html#index-0">dielectric</a>
</dt>
<dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
</dt>
<dt><a href="dihedral_style.html#index-0">dihedral_style</a>
</dt>
<dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
</dt>
<dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
</dt>
<dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
</dt>
<dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
</dt>
<dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
</dt>
<dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
</dt>
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
</dt>
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
</dt>
<dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
</dt>
<dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
</dt>
<dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
</dt>
<dt><a href="dimension.html#index-0">dimension</a>
</dt>
<dt><a href="displace_atoms.html#index-0">displace_atoms</a>
</dt>
<dt><a href="dump.html#index-0">dump</a>
</dt>
<dt><a href="dump_h5md.html#index-0">dump h5md</a>
</dt>
<dt><a href="dump_image.html#index-0">dump image</a>
</dt>
<dt><a href="dump_molfile.html#index-0">dump molfile</a>
</dt>
<dt><a href="dump_modify.html#index-0">dump_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="echo.html#index-0">echo</a>
</dt>
</dl></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix.html#index-0">fix</a>
</dt>
<dt><a href="fix_adapt.html#index-0">fix adapt</a>
</dt>
<dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
</dt>
<dt><a href="fix_addforce.html#index-0">fix addforce</a>
</dt>
<dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
</dt>
<dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
</dt>
<dt><a href="fix_atc.html#index-0">fix atc</a>
</dt>
<dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
</dt>
<dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
</dt>
<dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
</dt>
<dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
</dt>
<dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
</dt>
<dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
</dt>
<dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
</dt>
<dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
</dt>
<dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
</dt>
<dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
</dt>
<dt><a href="fix_balance.html#index-0">fix balance</a>
</dt>
<dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
</dt>
<dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
</dt>
<dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
</dt>
<dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
</dt>
<dt><a href="fix_colvars.html#index-0">fix colvars</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>
<dt><a href="fix_deposit.html#index-0">fix deposit</a>
</dt>
<dt><a href="fix_drag.html#index-0">fix drag</a>
</dt>
<dt><a href="fix_drude.html#index-0">fix drude</a>
</dt>
<dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
</dt>
<dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
</dt>
<dt><a href="fix_efield.html#index-0">fix efield</a>
</dt>
<dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
<dt><a href="fix_external.html#index-0">fix external</a>
</dt>
<dt><a href="fix_freeze.html#index-0">fix freeze</a>
</dt>
<dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
</dt>
<dt><a href="fix_gld.html#index-0">fix gld</a>
</dt>
<dt><a href="fix_gle.html#index-0">fix gle</a>
</dt>
<dt><a href="fix_gravity.html#index-0">fix gravity</a>
</dt>
<dt><a href="fix_heat.html#index-0">fix heat</a>
</dt>
<dt><a href="fix_imd.html#index-0">fix imd</a>
</dt>
<dt><a href="fix_indent.html#index-0">fix indent</a>
</dt>
<dt><a href="fix_ipi.html#index-0">fix ipi</a>
</dt>
<dt><a href="fix_langevin.html#index-0">fix langevin</a>
</dt>
<dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
</dt>
<dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
</dt>
<dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
</dt>
<dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
</dt>
<dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
</dt>
<dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
</dt>
<dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
</dt>
<dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
<dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
</dt>
<dt><a href="fix_momentum.html#index-0">fix momentum</a>
</dt>
<dt><a href="fix_move.html#index-0">fix move</a>
</dt>
<dt><a href="fix_msst.html#index-0">fix msst</a>
</dt>
<dt><a href="fix_neb.html#index-0">fix neb</a>
</dt>
<dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
</dt>
<dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
</dt>
<dt><a href="fix_nphug.html#index-0">fix nphug</a>
</dt>
<dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
</dt>
<dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>
<dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
</dt>
<dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
</dt>
<dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
</dt>
<dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
</dt>
<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
<dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
</dt>
<dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
</dt>
<dt><a href="fix_nh.html#index-0">fix nvt</a>
</dt>
<dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
</dt>
<dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
</dt>
<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
</dt>
<dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
</dt>
<dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
</dt>
<dt><a href="fix_oneway.html#index-0">fix oneway</a>
</dt>
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
</dt>
<dt><a href="fix_phonon.html#index-0">fix phonon</a>
</dt>
<dt><a href="fix_pimd.html#index-0">fix pimd</a>
</dt>
<dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
</dt>
<dt><a href="fix_pour.html#index-0">fix pour</a>
</dt>
<dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
</dt>
<dt><a href="fix_print.html#index-0">fix print</a>
</dt>
<dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
</dt>
<dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
</dt>
<dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
</dt>
<dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
</dt>
<dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
</dt>
<dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
</dt>
<dt><a href="fix_qtb.html#index-0">fix qtb</a>
</dt>
<dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
</dt>
<dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
</dt>
<dt><a href="fix_recenter.html#index-0">fix recenter</a>
</dt>
<dt><a href="fix_restrain.html#index-0">fix restrain</a>
</dt>
<dt><a href="fix_rigid.html#index-0">fix rigid</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
<dt><a href="fix_setforce.html#index-0">fix setforce</a>
</dt>
<dt><a href="fix_shake.html#index-0">fix shake</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
<dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
</dt>
<dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
</dt>
<dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
</dt>
<dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
</dt>
<dt><a href="fix_smd_setvel.html#index-0">fix smd/setvel</a>
</dt>
<dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
</dt>
<dt><a href="fix_spring.html#index-0">fix spring</a>
</dt>
<dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
</dt>
<dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
</dt>
<dt><a href="fix_srd.html#index-0">fix srd</a>
</dt>
<dt><a href="fix_store_force.html#index-0">fix store/force</a>
</dt>
<dt><a href="fix_store_state.html#index-0">fix store/state</a>
</dt>
<dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
</dt>
<dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
</dt>
<dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
</dt>
<dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
</dt>
<dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
</dt>
<dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
</dt>
<dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
</dt>
<dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
</dt>
<dt><a href="fix_tmd.html#index-0">fix tmd</a>
</dt>
<dt><a href="fix_ttm.html#index-0">fix ttm</a>
</dt>
<dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
</dt>
<dt><a href="fix_vector.html#index-0">fix vector</a>
</dt>
<dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
</dt>
<dt><a href="fix_viscous.html#index-0">fix viscous</a>
</dt>
<dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
</dt>
<dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
</dt>
<dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
</dt>
<dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
</dt>
<dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
</dt>
<dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
</dt>
<dt><a href="fix_modify.html#index-0">fix_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group.html#index-0">group</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group2ndx.html#index-0">group2ndx</a>
</dt>
</dl></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="if.html#index-0">if</a>
</dt>
<dt><a href="improper_coeff.html#index-0">improper_coeff</a>
</dt>
<dt><a href="improper_style.html#index-0">improper_style</a>
</dt>
<dt><a href="improper_class2.html#index-0">improper_style class2</a>
</dt>
<dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
</dt>
<dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
</dt>
<dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
</dt>
<dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
</dt>
<dt><a href="improper_none.html#index-0">improper_style none</a>
</dt>
<dt><a href="improper_ring.html#index-0">improper_style ring</a>
</dt>
<dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
</dt>
<dt><a href="include.html#index-0">include</a>
</dt>
<dt><a href="info.html#index-0">info</a>
</dt>
</dl></td>
</tr></table>
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="jump.html#index-0">jump</a>
</dt>
</dl></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_modify.html#index-0">kspace_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_style.html#index-0">kspace_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="label.html#index-0">label</a>
</dt>
<dt><a href="lattice.html#index-0">lattice</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="log.html#index-0">log</a>
</dt>
</dl></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="mass.html#index-0">mass</a>
</dt>
<dt><a href="min_modify.html#index-0">min_modify</a>
</dt>
<dt><a href="min_style.html#index-0">min_style</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="minimize.html#index-0">minimize</a>
</dt>
<dt><a href="molecule.html#index-0">molecule</a>
</dt>
</dl></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="neb.html#index-0">neb</a>
</dt>
<dt><a href="neigh_modify.html#index-0">neigh_modify</a>
</dt>
<dt><a href="neighbor.html#index-0">neighbor</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="newton.html#index-0">newton</a>
</dt>
<dt><a href="next.html#index-0">next</a>
</dt>
</dl></td>
</tr></table>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="package.html#index-0">package</a>
</dt>
<dt><a href="pair_coeff.html#index-0">pair_coeff</a>
</dt>
<dt><a href="pair_modify.html#index-0">pair_modify</a>
</dt>
<dt><a href="pair_style.html#index-0">pair_style</a>
</dt>
<dt><a href="pair_adp.html#index-0">pair_style adp</a>
</dt>
<dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
</dt>
<dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
</dt>
<dt><a href="pair_beck.html#index-0">pair_style beck</a>
</dt>
<dt><a href="pair_body.html#index-0">pair_style body</a>
</dt>
<dt><a href="pair_bop.html#index-0">pair_style bop</a>
</dt>
<dt><a href="pair_born.html#index-0">pair_style born</a>
</dt>
<dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
</dt>
<dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
</dt>
<dt><a href="pair_buck.html#index-0">pair_style buck</a>
</dt>
<dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
</dt>
<dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
</dt>
<dt><a href="pair_comb.html#index-0">pair_style comb</a>
</dt>
<dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
</dt>
<dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
</dt>
<dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
</dt>
<dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
</dt>
<dt><a href="pair_eam.html#index-0">pair_style eam</a>
</dt>
<dt><a href="pair_edip.html#index-0">pair_style edip</a>
</dt>
<dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
</dt>
<dt><a href="pair_eim.html#index-0">pair_style eim</a>
</dt>
<dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
</dt>
<dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
</dt>
<dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
</dt>
<dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
</dt>
<dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
</dt>
<dt><a href="pair_kim.html#index-0">pair_style kim</a>
</dt>
<dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
</dt>
<dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
</dt>
<dt><a href="pair_list.html#index-0">pair_style list</a>
</dt>
<dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
</dt>
<dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
</dt>
<dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
</dt>
<dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
</dt>
<dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
</dt>
<dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
</dt>
<dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
</dt>
<dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
</dt>
<dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
</dt>
<dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
</dt>
<dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
</dt>
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
<dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
</dt>
<dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
</dt>
<dt><a href="pair_meam.html#index-0">pair_style meam</a>
</dt>
+ <dt><a href="pair_mgpt.html#index-0">pair_style mgpt</a>
+ </dt>
+
+
<dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
</dt>
<dt><a href="pair_morse.html#index-0">pair_style morse</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>
<dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
</dt>
<dt><a href="pair_none.html#index-0">pair_style none</a>
</dt>
<dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
</dt>
<dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
</dt>
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+
+ <div class="section" id="pair-style-mgpt-command">
+<span id="index-0"></span><h1>pair_style mgpt command<a class="headerlink" href="#pair-style-mgpt-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>pair_style mgpt
+</pre></div>
+</div>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
+(<a class="reference internal" href="#moriarty1"><span>Moriarty1</span></a>) provides a first-principles approach to
+multi-ion interatomic potentials in d-band transition metals, with a
+volume-dependent, real-space total-energy functional for the N-ion
+elemental bulk material in the form</p>
+<img alt="_images/pair_mgpt.jpg" class="align-center" src="_images/pair_mgpt.jpg" />
+<p>where the prime on each summation sign indicates the exclusion of all
+self-interaction terms from the summation. The leading volume term
+E_vol as well as the two-ion central-force pair potential v_2 and the
+three- and four-ion angular-force potentials, v_3 and v_4, depend
+explicitly on the atomic volume Omega, but are structure independent
+and transferable to all bulk ion configurations, either ordered or
+disordered, and with of without the presence of point and line
+defects. The simplified model GPT or MGPT (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>,
+<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>), which retains the form of E_tot and permits
+more efficient large-scale atomistic simulations, derives from the GPT
+through a series of systematic approximations applied to E_vol and the
+potentials v_n that are valid for mid-period transition metals with
+nearly half-filled d bands.</p>
+<p>Both analytic (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>) and matrix
+(<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) representations of MGPT have been developed.
+In the more general matrix representation, which can also be applied
+to f-band actinide metals and permits both canonical and non-canonical
+d/f bands, 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. Fast matrix-MGPT
+algorithms have been developed independently by Glosli
+(<span class="xref std std-ref">Glosli</span>, <a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) and by Oppelstrup
+(<a class="reference internal" href="#oppelstrup"><span>Oppelstrup</span></a>)</p>
+<p>The <em>mgpt</em> pair style calculates forces, energies, and the total
+energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
+Input potential and control data are entered through the
+<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. Each material treated requires
+input parmin and potin potential files, as shown in the above
+examples, as well as specification by the user of the initial atomic
+volume Omega through pair_coeff. At the beginning of a time step in
+any simulation, the total volume of the simulation cell V should
+always be equal to Omega*N, where N is the number of metal ions
+present, taking into account the presence of any vacancies and/or
+interstitials in the case of a solid. In a constant-volume
+simulation, which is the normal mode of operation for the <em>mgpt</em> pair
+style, Omega, V and N all remain constant throughout the simulation
+and thus are equal to their initial values. In a constant-stress
+simulation, the cell volume V will change (slowly) as the simulation
+proceeds. After each time step, the atomic volume should be updated
+by the code as Omega = V/N. In addition, the volume term E_vol and
+the potentials v_2, v_3 and v_4 have to be removed at the end of the
+time step, and then respecified at the new value of Omega. In all
+smulations, Omega must remain within the defined volume range for
+E_vol and the potentials for the given material.</p>
+<p>The default option volpress yes in the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
+command includes all volume derivatives of E_tot required to calculate
+the stress tensor and pressure correctly. The option volpress no
+disregards the pressure contribution resulting from the volume term
+E_vol, and can be used for testing and analysis purposes. The
+additional optional variable nbody controls the specific terms in
+E_tot that are calculated. The default option and the normal option
+for mid-period transition and actinide metals is nbody 1234 for which
+all four terms in E_tot are retained. The option nbody 12, for
+example, retains only the volume term and the two-ion pair potential
+term and can be used for GPT series-end transition metals that can be
+well described without v_3 and v_4. The nbody option can also be used
+to test or analyze the contribution of any of the four terms in E_tot
+to a given calculated property.</p>
+<p>The <em>mgpt</em> pair style makes extensive use of matrix algebra and
+includes optimized kernels for the BlueGene/Q architecture and the
+Intel/AMD (x86) architectures. When compiled with the appropriate
+compiler and compiler switches (-msse3 on x86, and using the IBM XL
+compiler on BG/Q), these optimized routines are used automatically.
+For BG/Q machines, building with the default Makefile for that
+architecture (e.g., “make bgq”) should enable the optimized algebra
+routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
+(build with “make mpi_fastmgpt”) enables the fast algebra routines.
+The user will be informed in the output files of the matrix kernels in
+use. To further improve speed, on x86 the option precision single can
+be added to the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command line, which
+improves speed (up to a factor of two) at the cost of doing matrix
+calculations with 7 digit precision instead of the default 16. For
+consistency the default option can be specified explicitly by the
+option precision double.</p>
+<p>All remaining potential and control data are contained with the parmin
+and potin files, including cutoffs, atomic mass, and other basic MGPT
+variables. Specific MGPT potential data for the transition metals
+tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
+and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
+directory. The stored files are, respectively, Ta4.mgpt.parmin,
+Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
+Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
+V6.1.mgpt.potin . Useful corresponding informational “README” files
+on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
+potentials directory. These latter files indicate the volume mesh and
+range for each potential and give appropriate references for the
+potentials. It is expected that MGPT potentials for additional
+materials will be added over time.</p>
+<p>Useful example MGPT scripts are given in the examples/USER/mgpt
+directory. These scripts show the necessary steps to perform
+constant-volume calculations and simulations. It is strongly
+recommended that the user work through and understand these examples
+before proceeding to more complex simulations.</p>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">For good performance, LAMMPS should be built with the
+compiler flags “-O3 -msse3 -funroll-loops” when including this pair
+style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example
+machine Makefile with these options included as part of a standard MPI
+build. Note that as-is it will build with whatever low-level compiler
+(g++, icc, etc) is the default for your MPI installation.</p>
+</div>
+<hr class="docutils" />
+<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
+<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
+mix, shift, table, and tail options.</p>
+<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.</p>
+<p>This pair style can only be used via the <em>pair</em> keyword of the
+<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
+<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
+</div>
+<hr class="docutils" />
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<p>This pair style is part of the USER-MGPT package and is only enabled
+if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>The MGPT potentials require the <a class="reference internal" href="newton.html"><em>newtion</em></a> setting to be
+“on” for pair style interactions.</p>
+<p>The stored parmin and potin potential files provided with LAMMPS in
+the “potentials” directory are written in Rydberg atomic units, with
+energies in Rydbergs and distances in Bohr radii. The <em>mgpt</em> pair
+style converts Rydbergs to Hartrees to make the potential files
+compatible with LAMMPS electron <a class="reference internal" href="units.html"><em>units</em></a>.</p>
+<p>The form of E_tot used in the <em>mgpt</em> pair style is only appropriate
+for elemental bulk solids and liquids. This includes solids with
+point and extended defects such as vacancies, interstitials, grain
+boundaries and dislocations. Alloys and free surfaces, however,
+require significant modifications, which are not included in the
+<em>mgpt</em> pair style. Likewise, the <em>hybrid</em> pair style is not allowed,
+where MGPT would be used for some atoms but not for others.</p>
+<p>Electron-thermal effects are not included in the standard MGPT
+potentials provided in the “potentials” directory, where the
+potentials have been constructed at zero electron temperature.
+Physically, electron-thermal effects may be important in 3d (e.g., V)
+and 4d (e.g., Mo) transition metals at high temperatures near melt and
+above. It is expected that temperature-dependent MGPT potentials for
+such cases will be added over time.</p>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
+</div>
+<div class="section" id="default">
+<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
+<p>The options defaults for the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command are
+volpress yes, nbody 1234, and precision double.</p>
+<hr class="docutils" />
+<p id="moriarty1"><strong>(Moriarty1)</strong> Moriarty, Physical Review B, 38, 3199 (1988).</p>
+<p id="moriarty2"><strong>(Moriarty2)</strong> Moriarty, Physical Review B, 42, 1609 (1990).
+Moriarty, Physical Review B 49, 12431 (1994).</p>
+<p id="moriarty3"><strong>(Moriarty3)</strong> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
+Journal of Materials Research, 21, 563 (2006).</p>
+<p id="glosli"><strong>(Glosli)</strong> Glosli, unpublished, 2005.
+Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
+Series, 46, 254 (2006).</p>
+<p id="oppelstrup"><strong>(Oppelstrup)</strong> Oppelstrup, unpublished, 2015.
+Oppelstrup and Moriarty, to be published.</p>
+</div>
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diff --git a/doc/pair_mgpt.txt b/doc/pair_mgpt.txt
new file mode 100644
index 000000000..fc21a488c
--- /dev/null
+++ b/doc/pair_mgpt.txt
@@ -0,0 +1,219 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style mgpt command :h3
+
+[Syntax:]
+
+pair_style mgpt :pre
+
+[Examples:]
+
+pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12 :pre
+
+[Description:]
+
+Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
+("Moriarty1"_#Moriarty1) provides a first-principles approach to
+multi-ion interatomic potentials in d-band transition metals, with a
+volume-dependent, real-space total-energy functional for the N-ion
+elemental bulk material in the form
+
+:c,image(Eqs/pair_mgpt.jpg)
+
+where the prime on each summation sign indicates the exclusion of all
+self-interaction terms from the summation. The leading volume term
+E_vol as well as the two-ion central-force pair potential v_2 and the
+three- and four-ion angular-force potentials, v_3 and v_4, depend
+explicitly on the atomic volume Omega, but are structure independent
+and transferable to all bulk ion configurations, either ordered or
+disordered, and with of without the presence of point and line
+defects. The simplified model GPT or MGPT ("Moriarty2"_#Moriarty2,
+"Moriarty3"_#Moriarty3), which retains the form of E_tot and permits
+more efficient large-scale atomistic simulations, derives from the GPT
+through a series of systematic approximations applied to E_vol and the
+potentials v_n that are valid for mid-period transition metals with
+nearly half-filled d bands.
+
+Both analytic ("Moriarty2"_#Moriarty2) and matrix
+("Moriarty3"_#Moriarty3) representations of MGPT have been developed.
+In the more general matrix representation, which can also be applied
+to f-band actinide metals and permits both canonical and non-canonical
+d/f bands, 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. Fast matrix-MGPT
+algorithms have been developed independently by Glosli
+("Glosli"_#Glosi, "Moriarty3"_#Moriarty3) and by Oppelstrup
+("Oppelstrup"_#Oppelstrup)
+
+The {mgpt} pair style calculates forces, energies, and the total
+energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
+Input potential and control data are entered through the
+"pair_coeff"_pair_coeff.html command. Each material treated requires
+input parmin and potin potential files, as shown in the above
+examples, as well as specification by the user of the initial atomic
+volume Omega through pair_coeff. At the beginning of a time step in
+any simulation, the total volume of the simulation cell V should
+always be equal to Omega*N, where N is the number of metal ions
+present, taking into account the presence of any vacancies and/or
+interstitials in the case of a solid. In a constant-volume
+simulation, which is the normal mode of operation for the {mgpt} pair
+style, Omega, V and N all remain constant throughout the simulation
+and thus are equal to their initial values. In a constant-stress
+simulation, the cell volume V will change (slowly) as the simulation
+proceeds. After each time step, the atomic volume should be updated
+by the code as Omega = V/N. In addition, the volume term E_vol and
+the potentials v_2, v_3 and v_4 have to be removed at the end of the
+time step, and then respecified at the new value of Omega. In all
+smulations, Omega must remain within the defined volume range for
+E_vol and the potentials for the given material.
+
+The default option volpress yes in the "pair_coeff"_pair_coeff.html
+command includes all volume derivatives of E_tot required to calculate
+the stress tensor and pressure correctly. The option volpress no
+disregards the pressure contribution resulting from the volume term
+E_vol, and can be used for testing and analysis purposes. The
+additional optional variable nbody controls the specific terms in
+E_tot that are calculated. The default option and the normal option
+for mid-period transition and actinide metals is nbody 1234 for which
+all four terms in E_tot are retained. The option nbody 12, for
+example, retains only the volume term and the two-ion pair potential
+term and can be used for GPT series-end transition metals that can be
+well described without v_3 and v_4. The nbody option can also be used
+to test or analyze the contribution of any of the four terms in E_tot
+to a given calculated property.
+
+The {mgpt} pair style makes extensive use of matrix algebra and
+includes optimized kernels for the BlueGene/Q architecture and the
+Intel/AMD (x86) architectures. When compiled with the appropriate
+compiler and compiler switches (-msse3 on x86, and using the IBM XL
+compiler on BG/Q), these optimized routines are used automatically.
+For BG/Q machines, building with the default Makefile for that
+architecture (e.g., "make bgq") should enable the optimized algebra
+routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
+(build with "make mpi_fastmgpt") enables the fast algebra routines.
+The user will be informed in the output files of the matrix kernels in
+use. To further improve speed, on x86 the option precision single can
+be added to the "pair_coeff"_pair_coeff.html command line, which
+improves speed (up to a factor of two) at the cost of doing matrix
+calculations with 7 digit precision instead of the default 16. For
+consistency the default option can be specified explicitly by the
+option precision double.
+
+All remaining potential and control data are contained with the parmin
+and potin files, including cutoffs, atomic mass, and other basic MGPT
+variables. Specific MGPT potential data for the transition metals
+tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
+and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
+directory. The stored files are, respectively, Ta4.mgpt.parmin,
+Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
+Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
+V6.1.mgpt.potin . Useful corresponding informational "README" files
+on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
+potentials directory. These latter files indicate the volume mesh and
+range for each potential and give appropriate references for the
+potentials. It is expected that MGPT potentials for additional
+materials will be added over time.
+
+Useful example MGPT scripts are given in the examples/USER/mgpt
+directory. These scripts show the necessary steps to perform
+constant-volume calculations and simulations. It is strongly
+recommended that the user work through and understand these examples
+before proceeding to more complex simulations.
+
+IMPORTANT NOTE: For good performance, LAMMPS should be built with the
+compiler flags "-O3 -msse3 -funroll-loops" when including this pair
+style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example
+machine Makefile with these options included as part of a standard MPI
+build. Note that as-is it will build with whatever low-level compiler
+(g++, icc, etc) is the default for your MPI installation.
+
+:line
+
+[Mixing, shift, table tail correction, restart]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the USER-MGPT package and is only enabled
+if LAMMPS is built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+The MGPT potentials require the "newtion"_newton.html setting to be
+"on" for pair style interactions.
+
+The stored parmin and potin potential files provided with LAMMPS in
+the "potentials" directory are written in Rydberg atomic units, with
+energies in Rydbergs and distances in Bohr radii. The {mgpt} pair
+style converts Rydbergs to Hartrees to make the potential files
+compatible with LAMMPS electron "units"_units.html.
+
+The form of E_tot used in the {mgpt} pair style is only appropriate
+for elemental bulk solids and liquids. This includes solids with
+point and extended defects such as vacancies, interstitials, grain
+boundaries and dislocations. Alloys and free surfaces, however,
+require significant modifications, which are not included in the
+{mgpt} pair style. Likewise, the {hybrid} pair style is not allowed,
+where MGPT would be used for some atoms but not for others.
+
+Electron-thermal effects are not included in the standard MGPT
+potentials provided in the "potentials" directory, where the
+potentials have been constructed at zero electron temperature.
+Physically, electron-thermal effects may be important in 3d (e.g., V)
+and 4d (e.g., Mo) transition metals at high temperatures near melt and
+above. It is expected that temperature-dependent MGPT potentials for
+such cases will be added over time.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:]
+
+The options defaults for the "pair_coeff"_pair_coeff.html command are
+volpress yes, nbody 1234, and precision double.
+
+:line
+
+:link(Moriarty1)
+[(Moriarty1)] Moriarty, Physical Review B, 38, 3199 (1988).
+
+:link(Moriarty2)
+[(Moriarty2)] Moriarty, Physical Review B, 42, 1609 (1990).
+Moriarty, Physical Review B 49, 12431 (1994).
+
+:link(Moriarty3)
+[(Moriarty3)] Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
+Journal of Materials Research, 21, 563 (2006).
+
+:link(Glosli)
+[(Glosli)] Glosli, unpublished, 2005.
+Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
+Series, 46, 254 (2006).
+
+:link(Oppelstrup)
+[(Oppelstrup)] Oppelstrup, unpublished, 2015.
+Oppelstrup and Moriarty, to be published.
diff --git a/doc/pair_smtbq.html b/doc/pair_smtbq.html
new file mode 100644
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+++ b/doc/pair_smtbq.html
@@ -0,0 +1,428 @@
+
+
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+
+ <div class="section" id="pair-style-smtbq-command">
+<span id="index-0"></span><h1>pair_style smtbq command<a class="headerlink" href="#pair-style-smtbq-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>pair_style smtbq
+</pre></div>
+</div>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>This pair stylecomputes a variable charge SMTB-Q (Second-Moment
+tight-Binding QEq) potential as described in <a class="reference internal" href="#smtb-q-1"><span>SMTB-Q_1</span></a> and
+<a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a>. Briefly, the energy of metallic-oxygen systems
+is given by three contributions:</p>
+<img alt="_images/pair_smtbq1.jpg" class="align-center" src="_images/pair_smtbq1.jpg" />
+<p>where <em>E<sub>tot</sub></em> is the total potential energy of the system,
+<em>E<sub>ES</sub></em> is the electrostatic part of the total energy,
+<em>E<sub>OO</sub></em> is the interaction between oxygens and
+<em>E<sub>MO</sub></em> is a short-range interaction between metal and oxygen
+atoms. This interactions depend on interatomic distance
+<em>r<sub>ij</sub></em> and/or the charge <em>Q<sub>i</sub></em> of atoms
+<em>i</em>. Cut-off function enables smooth convergence to zero interaction.</p>
+<p>The parameters appearing in the upper expressions are set in the
+ffield.SMTBQ.Syst file where Syst corresponds to the selected system
+(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>,
+Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command
+is used with the SMTBQ styles which provides the path to the potential
+file with parameters for needed elements. These are mapped to LAMMPS
+atom types by specifying additional arguments after the potential
+filename in the pair_coeff command. Note that atom type 1 must always
+correspond to oxygen atoms. As an example, to simulate a TiO2 system,
+atom type 1 has to be oxygen and atom type 2 Ti. The following
+pair_coeff command should then be used:</p>
+<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+</pre></div>
+</div>
+<p>The electrostatic part of the energy consists of two components</p>
+<p>self-energy of atom <em>i</em> in the form of a second order charge dependent
+polynomial and a long-range Coulombic electrostatic interaction. The
+latter uses the wolf summation method described in <a class="reference internal" href="#wolf"><span>Wolf</span></a>,
+spherically truncated at a longer cutoff, <em>R<sub>coul</sub></em>. The
+charge of each ion is modeled by an orbital Slater which depends on
+the principal quantum number (<em>n</em>) of the outer orbital shared by the
+ion.</p>
+<p>Interaction between oxygen, <em>E<sub>OO</sub></em>, consists of two parts,
+an attractive and a repulsive part. The attractive part is effective
+only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive
+contribution was optimized to study surfaces reconstruction
+(e.g. <a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a> in TiO<sub>2</sub>) and is not necessary
+for oxide bulk modeling. The repulsive part is the Pauli interaction
+between the electron clouds of oxygen. The Pauli repulsion and the
+coulombic electrostatic interaction have same cut off value. In the
+ffield.SMTBQ.Syst, the keyword <em>‘buck’</em> allows to consider only the
+repulsive O-O interactions. The keyword <em>‘buckPlusAttr’</em> allows to
+consider the repulsive and the attractive O-O interactions.</p>
+<p>The short-range interaction between metal-oxygen, <em>E<sub>MO</sub></em> is
+based on the second moment approximation of the density of states with
+a N-body potential for the band energy term,
+<em>E<sup>i</sup><sub>cov</sub></em>, and a Born-Mayer type repulsive terms
+as indicated by the keyword <em>‘second_moment’</em> in the
+ffield.SMTBQ.Syst. The energy band term is given by:</p>
+<img alt="_images/pair_smtbq2.jpg" class="align-center" src="_images/pair_smtbq2.jpg" />
+<p>where <em>&#951<sub>i</sub></em> is the stoichiometry of atom <em>i</em>,
+<em>&#948Q<sub>i</sub></em> is the charge delocalization of atom <em>i</em>,
+compared to its formal charge
+<em>Q<sup>F</sup><sub>i</sub></em>. n<sub>0</sub>, the number of hybridized
+orbitals, is calculated with to the atomic orbitals shared
+<em>d<sub>i</sub></em> and the stoichiometry
+<em>&#951<sub>i</sub></em>. <em>r<sub>c1</sub></em> and <em>r<sub>c2</sub></em> are the two
+cutoff radius around the fourth neighbors in the cutoff function.</p>
+<p>In the formalism used here, <em>&#958<sup>0</sup></em> is the energy
+parameter. <em>&#958<sup>0</sup></em> is in tight-binding approximation the
+hopping integral between the hybridized orbitals of the cation and the
+anion. In the literature we find many ways to write the hopping
+integral depending on whether one takes the point of view of the anion
+or cation. These are equivalent vision. The correspondence between the
+two visions is explained in appendix A of the article in the
+SrTiO<sub>3</sub> <a class="reference internal" href="#smtb-q-3"><span>SMTB-Q_3</span></a> (parameter <em>&#946</em> shown in
+this article is in fact the <em>&#946<sub>O</sub></em>). To summarize the
+relationship between the hopping integral <em>&#958<sup>0</sup></em> and the
+others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following
+relationship:</p>
+<img alt="_images/pair_smtbq3.jpg" class="align-center" src="_images/pair_smtbq3.jpg" />
+<p>Thus parameter &#956, indicated above, is given by : &#956 = (&#8730n
++ &#8730m) &#8260 2</p>
+<p>The potential offers the possibility to consider the polarizability of
+the electron clouds of oxygen by changing the slater radius of the
+charge density around the oxygens through the parameters <em>rBB, rB and
+rS</em> in the ffield.SMTBQ.Syst. This change in radius is performed
+according to the method developed by E. Maras
+<a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a>. This method needs to determine the number of
+nearest neighbors around the oxygen. This calculation is based on
+first (<em>r<sub>1n</sub></em>) and second (<em>r<sub>2n</sub></em>) distances
+neighbors.</p>
+<p>The SMTB-Q potential is a variable charge potential. The equilibrium
+charge on each atom is calculated by the electronegativity
+equalization (QEq) method. See <a class="reference internal" href="#rick"><span>Rick</span></a> for further detail. One
+can adjust the frequency, the maximum number of iterative loop and the
+convergence of the equilibrium charge calculation. To obtain the
+energy conservation in NVE thermodynamic ensemble, we recommend to use
+a convergence parameter in the interval 10<sup>-5</sup> -
+10<sup>-6</sup> eV.</p>
+<p>The ffield.SMTBQ.Syst files are provided for few systems. They consist
+of nine parts and the lines beginning with ‘#’ are comments (note that
+the number of comment lines matter). The first sections are on the
+potential parameters and others are on the simulation options and
+might be modified. Keywords are character type and must be enclosed in
+quotation marks (‘’).</p>
+<ol class="arabic simple">
+<li>Number of different element in the oxide:</li>
+</ol>
+<ul class="simple">
+<li>N<sub>elem</sub>= 2 or 3</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="2">
+<li>Atomic parameters</li>
+</ol>
+<p>For the anion (oxygen)</p>
+<ul class="simple">
+<li>Name of element (char) and stoichiometry in oxide</li>
+<li>Formal charge and mass of element</li>
+<li>Principal quantic number of outer orbital (<em>n</em>), electronegativity (<em>&#967<sup>0</sup><sub>i</simulationub></em>) and hardness (<em>J<sup>0</sup><sub>i</sub></em>)</li>
+<li>Ionic radius parameters : max coordination number (<em>coordBB</em> = 6 by default), bulk coordination number <em>(coordB)</em>, surface coordination number <em>(coordS)</em> and <em>rBB, rB and rS</em> the slater radius for each coordination number. (<b>note : If you don’t want to change the slater radius, use three identical radius values</b>)</li>
+<li>Number of orbital shared by the element in the oxide (<em>d<sub>i</sub></em>)</li>
+<li>Divided line</li>
+</ul>
+<p>For each cations (metal):</p>
+<ul class="simple">
+<li>Name of element (char) and stoichiometry in oxide</li>
+<li>Formal charge and mass of element</li>
+<li>Number of electron in outer orbital <em>(ne)</em>, electronegativity (<em>&#967<sup>0</sup><sub>i</simulationub></em>), hardness (<em>J<sup>0</sup><sub>i</sub></em>) and <em>r<sub>Salter</sub></em> the slater radius for the cation.</li>
+<li>Number of orbitals shared by the elements in the oxide (<em>d<sub>i</sub></em>)</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="3">
+<li>Potential parameters:</li>
+</ol>
+<ul class="simple">
+<li>Keyword for element1, element2 and interaction potential (‘second_moment’ or ‘buck’ or ‘buckPlusAttr’) between element 1 and 2. If the potential is ‘second_moment’, specify ‘oxide’ or ‘metal’ for metal-oxygen or metal-metal interactions respectively.</li>
+<li>Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : <em>A (eV)</em>, <em>p</em>, <em>&#958<sup>0</sup></em> (eV) and <em>q</em> <br/> <em>r<sub>c1</sub></em> (&#197), <em>r<sub>c2</sub></em> (&#197) and <em>r<sub>0</sub></em> (&#197) <br/> If type of potential is ‘buck’ : <em>C</em> (eV) and <em>&#961</em> (&#197) <br/> If type of potential is ‘buckPlusAttr’ : <em>C</em> (eV) and <em>&#961</em> (&#197) <br/> <em>D</em> (eV), <em>B</em> (&#197<sup>-1</sup>), <em>r<sub>1</sub><sup>OO</sup></em> (&#197) and <em>r<sub>2</sub><sup>OO</sup></em> (&#197) </pre></li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="4">
+<li>Tables parameters:</li>
+</ol>
+<ul class="simple">
+<li>Cutoff radius for the Coulomb interaction (<em>R<sub>coul</sub></em>)</li>
+<li>Starting radius (<em>r<sub>min</sub></em> = 1,18845 &#197) and increments (<em>dr</em> = 0,001 &#197) for creating the potential table.</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="5">
+<li>Rick model parameter:</li>
+</ol>
+<ul class="simple">
+<li><em>Nevery</em> : parameter to set the frequency (<em>1/Nevery</em>) of the charge resolution. The charges are evaluated each <em>Nevery</em> time steps.</li>
+<li>Max number of iterative loop (<em>loopmax</em>) and precision criterion (<em>prec</em>) in eV of the charge resolution</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="6">
+<li>Coordination parameter:</li>
+</ol>
+<ul class="simple">
+<li>First (<em>r<sub>1n</sub></em>) and second (<em>r<sub>2n</sub></em>) neighbor distances in &#197</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="7">
+<li>Charge initialization mode:</li>
+</ol>
+<ul class="simple">
+<li>Keyword (<em>QInitMode</em>) and initial oxygen charge (<em>Q<sub>init</sub></em>). If keyword = ‘true’, all oxygen charges are initially set equal to <em>Q<sub>init</sub></em>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = ‘false’, all atom charges are initially set equal to 0 if you use “create_atom”#create_atom command or the charge specified in the file structure using <span class="xref std std-ref">read_data</span> command.</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="8">
+<li>Mode for the electronegativity equalization (Qeq)</li>
+</ol>
+<ul class="simple">
+<li>Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre></li>
+<li>Parameter if necessary</li>
+<li>Divided line</li>
+</ul>
+<ol class="arabic simple" start="9">
+<li>Verbose</li>
+</ol>
+<ul class="simple">
+<li>If you want the code to work in verbose mode or not : ‘true’ or ‘false’</li>
+<li>If you want to print or not in file ‘Energy_component.txt’ the three main contributions to the energy of the system according to the description presented above : ‘true’ or ‘false’ and <em>N<sub>Energy</sub></em>. This option writes in file every <em>N<sub>Energy</sub></em> time step. If the value is ‘false’ then <em>N<sub>Energy</sub></em> = 0. The file take into account the possibility to have several QEq group <em>g</em> then it writes: time step, number of atoms in group <em>g</em>, electrostatic part of energy, <em>E<sub>ES</sub></em>, the interaction between oxygen, <em>E<sub>OO</sub></em>, and short range metal-oxygen interaction, <em>E<sub>MO</sub></em>.</li>
+<li>If you want to print in file ‘Electroneg_component.txt’ the electronegativity component (<em>&#8706E<sub>tot</sub> &#8260&#8706Q<sub>i</sub></em>) or not: ‘true’ or ‘false’ and <em>N<sub>Electroneg</sub></em>.This option writes in file every <em>N<sub>Electroneg</sub></em> time step. If the value is ‘false’ then <em>N<sub>Electroneg</sub></em> = 0. The file consist in atom number <em>i</em>, atom type (1 for oxygen and # higher than 1 for metal), atom position: <em>x</em>, <em>y</em> and <em>z</em>, atomic charge of atom <em>i</em>, electrostatic part of atom <em>i</em> electronegativity, covalent part of atom <em>i</em> electronegativity, the hopping integral of atom <em>i</em> <em>(Z&#946<sup>2</sup>)<sub>i<sub></em> and box electronegativity.</li>
+</ul>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">This last option slows down the calculation
+dramatically. Use only with a single processor simulation.</p>
+</div>
+<hr class="docutils" />
+<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info:</strong></p>
+<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
+mix, shift, table, and tail options.</p>
+<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.</p>
+<p>This pair style can only be used via the <em>pair</em> keyword of the
+<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
+<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
+<hr class="docutils" />
+<p><strong>Restriction:</strong></p>
+<p>This pair style is part of the USER-SMTBQ package and is only enabled
+if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>This potential requires using atom type 1 for oxygen and atom type
+higher than 1 for metal atoms.</p>
+<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be “on”
+for pair interactions.</p>
+<p>The SMTB-Q potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal <code class="xref doc docutils literal"><span class="pre">units</span></code>.</p>
+<hr class="docutils" />
+<p><strong>Citing this work:</strong></p>
+<p>Please cite related publication: N. Salles, O. Politano, E. Amzallag
+and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189</p>
+<hr class="docutils" />
+<p id="smtb-q-1"><strong>(SMTB-Q_1)</strong> N. Salles, O. Politano, E. Amzallag, R. Tetot,
+Comput. Mater. Sci. 111 (2016) 181-189</p>
+<p id="smtb-q-2"><strong>(SMTB-Q_2)</strong> E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
+H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399</p>
+<p id="smtb-q-3"><strong>(SMTB-Q_3)</strong> R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
+Science 616, 19-8722 28 (2013)</p>
+<p id="wolf"><strong>(Wolf)</strong> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).</p>
+<p id="rick"><strong>(Rick)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).</p>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright .
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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diff --git a/doc/pair_smtbq.txt b/doc/pair_smtbq.txt
new file mode 100755
index 000000000..8dc612ed9
--- /dev/null
+++ b/doc/pair_smtbq.txt
@@ -0,0 +1,261 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style smtbq command :h3
+
+[Syntax:]
+
+pair_style smtbq :pre
+
+[Examples:]
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al :pre
+
+[Description:]
+
+This pair stylecomputes a variable charge SMTB-Q (Second-Moment
+tight-Binding QEq) potential as described in "SMTB-Q_1"_#SMTB-Q_1 and
+"SMTB-Q_2"_#SMTB-Q_2. Briefly, the energy of metallic-oxygen systems
+is given by three contributions:
+
+:c,image(Eqs/pair_smtbq1.jpg)
+
+where {E<sub>tot</sub>} is the total potential energy of the system,
+{E<sub>ES</sub>} is the electrostatic part of the total energy,
+{E<sub>OO</sub>} is the interaction between oxygens and
+{E<sub>MO</sub>} is a short-range interaction between metal and oxygen
+atoms. This interactions depend on interatomic distance
+{r<sub>ij</sub>} and/or the charge {Q<sub>i</sub>} of atoms
+{i}. Cut-off function enables smooth convergence to zero interaction.
+
+The parameters appearing in the upper expressions are set in the
+ffield.SMTBQ.Syst file where Syst corresponds to the selected system
+(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>,
+Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command
+is used with the SMTBQ styles which provides the path to the potential
+file with parameters for needed elements. These are mapped to LAMMPS
+atom types by specifying additional arguments after the potential
+filename in the pair_coeff command. Note that atom type 1 must always
+correspond to oxygen atoms. As an example, to simulate a TiO2 system,
+atom type 1 has to be oxygen and atom type 2 Ti. The following
+pair_coeff command should then be used:
+
+pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti :pre
+
+The electrostatic part of the energy consists of two components :
+self-energy of atom {i} in the form of a second order charge dependent
+polynomial and a long-range Coulombic electrostatic interaction. The
+latter uses the wolf summation method described in "Wolf"_#Wolf,
+spherically truncated at a longer cutoff, {R<sub>coul</sub>}. The
+charge of each ion is modeled by an orbital Slater which depends on
+the principal quantum number ({n}) of the outer orbital shared by the
+ion.
+
+Interaction between oxygen, {E<sub>OO</sub>}, consists of two parts,
+an attractive and a repulsive part. The attractive part is effective
+only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive
+contribution was optimized to study surfaces reconstruction
+(e.g. "SMTB-Q_2"_#SMTB-Q_2 in TiO<sub>2</sub>) and is not necessary
+for oxide bulk modeling. The repulsive part is the Pauli interaction
+between the electron clouds of oxygen. The Pauli repulsion and the
+coulombic electrostatic interaction have same cut off value. In the
+ffield.SMTBQ.Syst, the keyword {'buck'} allows to consider only the
+repulsive O-O interactions. The keyword {'buckPlusAttr'} allows to
+consider the repulsive and the attractive O-O interactions.
+
+The short-range interaction between metal-oxygen, {E<sub>MO</sub>} is
+based on the second moment approximation of the density of states with
+a N-body potential for the band energy term,
+{E<sup>i</sup><sub>cov</sub>}, and a Born-Mayer type repulsive terms
+as indicated by the keyword {'second_moment'} in the
+ffield.SMTBQ.Syst. The energy band term is given by:
+
+:c,image(Eqs/pair_smtbq2.jpg)
+
+where {η<sub>i</sub>} is the stoichiometry of atom {i},
+{δQ<sub>i</sub>} is the charge delocalization of atom {i},
+compared to its formal charge
+{Q<sup>F</sup><sub>i</sub>}. n<sub>0</sub>, the number of hybridized
+orbitals, is calculated with to the atomic orbitals shared
+{d<sub>i</sub>} and the stoichiometry
+{η<sub>i</sub>}. {r<sub>c1</sub>} and {r<sub>c2</sub>} are the two
+cutoff radius around the fourth neighbors in the cutoff function.
+
+In the formalism used here, {ξ<sup>0</sup>} is the energy
+parameter. {ξ<sup>0</sup>} is in tight-binding approximation the
+hopping integral between the hybridized orbitals of the cation and the
+anion. In the literature we find many ways to write the hopping
+integral depending on whether one takes the point of view of the anion
+or cation. These are equivalent vision. The correspondence between the
+two visions is explained in appendix A of the article in the
+SrTiO<sub>3</sub> "SMTB-Q_3"_#SMTB-Q_3 (parameter {β} shown in
+this article is in fact the {β<sub>O</sub>}). To summarize the
+relationship between the hopping integral {ξ<sup>0</sup>} and the
+others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following
+relationship:
+
+:c,image(Eqs/pair_smtbq3.jpg)
+
+Thus parameter μ, indicated above, is given by : μ = (√n
++ √m) ⁄ 2
+
+The potential offers the possibility to consider the polarizability of
+the electron clouds of oxygen by changing the slater radius of the
+charge density around the oxygens through the parameters {rBB, rB and
+rS} in the ffield.SMTBQ.Syst. This change in radius is performed
+according to the method developed by E. Maras
+"SMTB-Q_2"_#SMTB-Q_2. This method needs to determine the number of
+nearest neighbors around the oxygen. This calculation is based on
+first ({r<sub>1n</sub>}) and second ({r<sub>2n</sub>}) distances
+neighbors.
+
+The SMTB-Q potential is a variable charge potential. The equilibrium
+charge on each atom is calculated by the electronegativity
+equalization (QEq) method. See "Rick"_#Rick for further detail. One
+can adjust the frequency, the maximum number of iterative loop and the
+convergence of the equilibrium charge calculation. To obtain the
+energy conservation in NVE thermodynamic ensemble, we recommend to use
+a convergence parameter in the interval 10<sup>-5</sup> -
+10<sup>-6</sup> eV.
+
+The ffield.SMTBQ.Syst files are provided for few systems. They consist
+of nine parts and the lines beginning with '#' are comments (note that
+the number of comment lines matter). The first sections are on the
+potential parameters and others are on the simulation options and
+might be modified. Keywords are character type and must be enclosed in
+quotation marks ('').
+
+1) Number of different element in the oxide:
+
+N<sub>elem</sub>= 2 or 3
+Divided line :ul
+
+2) Atomic parameters
+
+For the anion (oxygen) :
+
+Name of element (char) and stoichiometry in oxide
+Formal charge and mass of element
+Principal quantic number of outer orbital ({n}), electronegativity ({χ<sup>0</sup><sub>i</simulationub>}) and hardness ({J<sup>0</sup><sub>i</sub>})
+ Ionic radius parameters : max coordination number ({coordBB} = 6 by default), bulk coordination number {(coordB)}, surface coordination number {(coordS)} and {rBB, rB and rS} the slater radius for each coordination number. (<b>note : If you don't want to change the slater radius, use three identical radius values</b>)
+Number of orbital shared by the element in the oxide ({d<sub>i</sub>})
+Divided line :ul
+
+For each cations (metal):
+
+Name of element (char) and stoichiometry in oxide
+Formal charge and mass of element
+Number of electron in outer orbital {(ne)}, electronegativity ({χ<sup>0</sup><sub>i</simulationub>}), hardness ({J<sup>0</sup><sub>i</sub>}) and {r<sub>Salter</sub>} the slater radius for the cation.
+Number of orbitals shared by the elements in the oxide ({d<sub>i</sub>})
+Divided line :ul
+
+3) Potential parameters:
+
+Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
+Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (Å), {r<sub>c2</sub>} (Å) and {r<sub>0</sub>} (Å) <br/> If type of potential is 'buck' : {C} (eV) and {ρ} (Å) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) <br/> {D} (eV), {B} (Å<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (Å) and {r<sub>2</sub><sup>OO</sup>} (Å) </pre>
+Divided line :ul
+
+4) Tables parameters:
+
+Cutoff radius for the Coulomb interaction ({R<sub>coul</sub>})
+Starting radius ({r<sub>min</sub>} = 1,18845 Å) and increments ({dr} = 0,001 Å) for creating the potential table.
+Divided line :ul
+
+5) Rick model parameter:
+
+{Nevery} : parameter to set the frequency ({1/Nevery}) of the charge resolution. The charges are evaluated each {Nevery} time steps.
+Max number of iterative loop ({loopmax}) and precision criterion ({prec}) in eV of the charge resolution
+Divided line :ul
+
+6) Coordination parameter:
+
+First ({r<sub>1n</sub>}) and second ({r<sub>2n</sub>}) neighbor distances in Å
+Divided line :ul
+
+7) Charge initialization mode:
+
+Keyword ({QInitMode}) and initial oxygen charge ({Q<sub>init</sub>}). If keyword = 'true', all oxygen charges are initially set equal to {Q<sub>init</sub>}. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using "read_data"_#read_data.html command.
+Divided line :ul
+
+8) Mode for the electronegativity equalization (Qeq) :
+
+Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
+Parameter if necessary
+Divided line :ul
+
+9) Verbose :
+
+If you want the code to work in verbose mode or not : 'true' or 'false'
+If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and {N<sub>Energy</sub>}. This option writes in file every {N<sub>Energy</sub>} time step. If the value is 'false' then {N<sub>Energy</sub>} = 0. The file take into account the possibility to have several QEq group {g} then it writes: time step, number of atoms in group {g}, electrostatic part of energy, {E<sub>ES</sub>}, the interaction between oxygen, {E<sub>OO</sub>}, and short range metal-oxygen interaction, {E<sub>MO</sub>}.
+If you want to print in file 'Electroneg_component.txt' the electronegativity component ({∂E<sub>tot</sub> ⁄∂Q<sub>i</sub>}) or not: 'true' or 'false' and {N<sub>Electroneg</sub>}.This option writes in file every {N<sub>Electroneg</sub>} time step. If the value is 'false' then {N<sub>Electroneg</sub>} = 0. The file consist in atom number {i}, atom type (1 for oxygen and # higher than 1 for metal), atom position: {x}, {y} and {z}, atomic charge of atom {i}, electrostatic part of atom {i} electronegativity, covalent part of atom {i} electronegativity, the hopping integral of atom {i} {(Zβ<sup>2</sup>)<sub>i<sub>} and box electronegativity. :ul
+
+IMPORTANT NOTE: This last option slows down the calculation
+dramatically. Use only with a single processor simulation.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info:]
+
+This pair style does not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files. Thus, you
+needs to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restriction:]
+
+This pair style is part of the USER-SMTBQ package and is only enabled
+if LAMMPS is built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This potential requires using atom type 1 for oxygen and atom type
+higher than 1 for metal atoms.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
+
+The SMTB-Q potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal "units"_unit.html.
+
+:line
+
+[Citing this work:]
+
+Please cite related publication: N. Salles, O. Politano, E. Amzallag
+and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+
+:line
+
+:link(SMTB-Q_1)
+[(SMTB-Q_1)] N. Salles, O. Politano, E. Amzallag, R. Tetot,
+Comput. Mater. Sci. 111 (2016) 181-189
+
+:link(SMTB-Q_2)
+[(SMTB-Q_2)] E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
+H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
+
+:link(SMTB-Q_3)
+[(SMTB-Q_3)] R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
+Science 616, 19-8722 28 (2013)
+
+:link(Wolf)
+[(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).
+
+:link(Rick)
+[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).
diff --git a/doc/searchindex.js b/doc/searchindex.js
index b13413c7a..8ed78e919 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:47,filenames:["Manual","Section_accelerate","Section_commands","Section_errors","Section_example","Section_history","Section_howto","Section_intro","Section_modify","Section_packages","Section_perf","Section_python","Section_start","Section_tools","accelerate_cuda","accelerate_gpu","accelerate_intel","accelerate_kokkos","accelerate_omp","accelerate_opt","angle_charmm","angle_class2","angle_coeff","angle_cosine","angle_cosine_delta","angle_cosine_periodic","angle_cosine_shift","angle_cosine_shift_exp","angle_cosine_squared","angle_dipole","angle_fourier","angle_fourier_simple","angle_harmonic","angle_hybrid","angle_none","angle_quartic","angle_sdk","angle_style","angle_table","atom_modify","atom_style","balance","body","bond_class2","bond_coeff","bond_fene","bond_fene_expand","bond_harmonic","bond_harmonic_shift","bond_harmonic_shift_cut","bond_hybrid","bond_morse","bond_none","bond_nonlinear","bond_quartic","bond_style","bond_table","boundary","box","change_box","clear","comm_modify","comm_style","compute","compute_ackland_atom","compute_angle_local","compute_angmom_chunk","compute_basal_atom","compute_body_local","compute_bond_local","compute_centro_atom","compute_chunk_atom","compute_cluster_atom","compute_cna_atom","compute_com","compute_com_chunk","compute_contact_atom","compute_coord_atom","compute_damage_atom","compute_dihedral_local","compute_dilatation_atom","compute_displace_atom","compute_erotate_asphere","compute_erotate_rigid","compute_erotate_sphere","compute_erotate_sphere_atom","compute_event_displace","compute_fep","compute_group_group","compute_gyration","compute_gyration_chunk","compute_heat_flux","compute_improper_local","compute_inertia_chunk","compute_ke","compute_ke_atom","compute_ke_atom_eff","compute_ke_eff","compute_ke_rigid","compute_meso_e_atom","compute_meso_rho_atom","compute_meso_t_atom","compute_modify","compute_msd","compute_msd_chunk","compute_msd_nongauss","compute_omega_chunk","compute_pair","compute_pair_local","compute_pe","compute_pe_atom","compute_plasticity_atom","compute_pressure","compute_property_atom","compute_property_chunk","compute_property_local","compute_rdf","compute_reduce","compute_saed","compute_slice","compute_smd_contact_radius","compute_smd_damage","compute_smd_hourglass_error","compute_smd_internal_energy","compute_smd_plastic_strain","compute_smd_plastic_strain_rate","compute_smd_rho","compute_smd_tlsph_defgrad","compute_smd_tlsph_dt","compute_smd_tlsph_num_neighs","compute_smd_tlsph_shape","compute_smd_tlsph_strain","compute_smd_tlsph_strain_rate","compute_smd_tlsph_stress","compute_smd_triangle_mesh_vertices","compute_smd_ulsph_num_neighs","compute_smd_ulsph_strain","compute_smd_ulsph_strain_rate","compute_smd_ulsph_stress","compute_smd_vol","compute_sna_atom","compute_stress_atom","compute_tally","compute_temp","compute_temp_asphere","compute_temp_chunk","compute_temp_com","compute_temp_cs","compute_temp_deform","compute_temp_deform_eff","compute_temp_drude","compute_temp_eff","compute_temp_partial","compute_temp_profile","compute_temp_ramp","compute_temp_region","compute_temp_region_eff","compute_temp_rotate","compute_temp_sphere","compute_ti","compute_torque_chunk","compute_vacf","compute_vcm_chunk","compute_voronoi_atom","compute_xrd","create_atoms","create_bonds","create_box","delete_atoms","delete_bonds","dielectric","dihedral_charmm","dihedral_class2","dihedral_coeff","dihedral_cosine_shift_exp","dihedral_fourier","dihedral_harmonic","dihedral_helix","dihedral_hybrid","dihedral_multi_harmonic","dihedral_nharmonic","dihedral_none","dihedral_opls","dihedral_quadratic","dihedral_style","dihedral_table","dimension","displace_atoms","dump","dump_h5md","dump_image","dump_modify","dump_molfile","echo","fix","fix_adapt","fix_adapt_fep","fix_addforce","fix_addtorque","fix_append_atoms","fix_atc","fix_atom_swap","fix_ave_atom","fix_ave_chunk","fix_ave_correlate","fix_ave_correlate_long","fix_ave_histo","fix_ave_spatial","fix_ave_spatial_sphere","fix_ave_time","fix_aveforce","fix_balance","fix_bond_break","fix_bond_create","fix_bond_swap","fix_box_relax","fix_colvars","fix_deform","fix_deposit","fix_drag","fix_drude","fix_drude_transform","fix_dt_reset","fix_efield","fix_enforce2d","fix_evaporate","fix_external","fix_freeze","fix_gcmc","fix_gld","fix_gle","fix_gravity","fix_heat","fix_imd","fix_indent","fix_ipi","fix_langevin","fix_langevin_drude","fix_langevin_eff","fix_lb_fluid","fix_lb_momentum","fix_lb_pc","fix_lb_rigid_pc_sphere","fix_lb_viscous","fix_lineforce","fix_meso","fix_meso_stationary","fix_modify","fix_momentum","fix_move","fix_msst","fix_neb","fix_nh","fix_nh_eff","fix_nph_asphere","fix_nph_sphere","fix_nphug","fix_npt_asphere","fix_npt_sphere","fix_nve","fix_nve_asphere","fix_nve_asphere_noforce","fix_nve_body","fix_nve_eff","fix_nve_limit","fix_nve_line","fix_nve_noforce","fix_nve_sphere","fix_nve_tri","fix_nvt_asphere","fix_nvt_sllod","fix_nvt_sllod_eff","fix_nvt_sphere","fix_oneway","fix_orient_fcc","fix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"_compute_t":8,"_j1m1m1":140,"_j2m2m2":140,"_serial":12,"abstract":17,"boolean":[3,331,333],"break":[],"byte":[3,12,205,475],"case":[1,2,3,6,8,9,11,12,13,15,16,17,18,39,40,41,45,46,59,61,63,71,73,104,108,114,116,117,143,144,145,146,148,151,152,153,154,155,157,158,159,163,165,167,168,169,171,188,189,190,191,197,198,202,203,204,206,207,208,209,210,211,213,215,217,221,223,225,228,231,232,234,235,236,237,239,250,252,253,254,255,256,257,258,269,270,272,274,275,280,282,283,284,285,292,293,295,297,299,300,302,305,308,311,312,313,315,316,320,322,323,325,326,328,329,330,331,333,347,348,349,351,353,355,356,357,358,360,362,363,365,374,377,379,381,385,387,390,391,393,394,395,397,407,408,409,410,414,416,420,423,426,428,431,438,441,442,444,451,453,456,458,460,461,465,466,468,470,472,474,475,476,477,479,483,484,485,487,488],"catch":[1,3,456],"char":[6,8],"class":[1,3,5,6,7,8,9,11,12,13,22,37,44,55,173,184,226,282,335,343,375,394,422,423,439,447,456,458],"default":[],"export":[190,376],"final":[3,5,6,7,8,11,12,17,41,59,87,141,191,202,203,204,206,207,208,209,211,215,217,228,251,252,256,283,287,293,294,297,317,319,320,327,333,356,358,364,365,369,385,388,395,407,410,416,420,421,440,441,442,444,447,453,466,472,479,484,486],"float":[3,6,8,12,40,42,71,113,188,191,203,209,233,282,294,310,387,427,429,456,458,468,475,484],"function":[],"import":[1,2,3,6,11,17,18,71,87,105,165,176,194,203,207,215,228,231,236,237,252,288,293,311,312,313,315,320,330,332,358,394,407,456,458,467,475,479],"int":[3,6,8,11,101,226,228,236,238,288,320,475],"long":[],"new":[],"null":[3,6,91,112,141,165,194,210,216,219,222,249,282,291,295,297,301,302,305,306,326,364,365,378,385,388,391,394,395,396,410,411,412,416,420,422,423,430,440,442,443,444,447,458,461,466,468,485],"public":[0,7,8,12,226,235,388,421],"return":[2,3,6,8,11,14,15,16,17,18,19,41,71,108,117,134,135,139,163,165,191,203,207,208,217,226,333,345,347,391,455,456,457,465,468,474,484],"short":[1,3,6,7,13,16,163,252,293,308,321,349,359,360,363,365,369,370,372,373,374,378,379,381,387,394,399,403,407,410,414,417,425,441,445,453,456,466,468,472,479],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,91,109,112,140,143,152,164,171,172,174,175,176,177,179,180,182,183,185,190,193,197,201,210,217,224,227,231,235,236,239,252,254,255,256,257,258,259,267,269,270,272,285,293,295,296,311,313,317,318,324,328,334,336,337,338,339,342,344,345,347,349,352,358,362,363,364,365,367,370,371,372,373,374,375,377,378,379,382,383,385,386,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,415,416,417,419,422,424,425,431,440,441,442,443,444,446,447,449,450,451,452,453,455,458,460,465,467,471,473,484,486,488],"throw":475,"true":[6,12,13,17,108,115,188,211,213,217,252,253,274,275,276,280,293,315,319,331,333,363,387,391,440,456,460,468,484],"try":[1,3,8,12,17,19,203,233,239,316,317,318,323,456,484],"var":[3,11,12,165,331,347,469,484],"void":[4,6,7,8,41,168,211,226,461],"while":[1,3,9,10,11,12,13,14,18,71,105,140,148,163,176,188,192,201,208,215,217,221,229,230,235,236,237,239,252,270,283,288,290,321,349,356,363,369,380,385,423,442,444,447,453,456,467,472,479],a10:333,a123:333,a12:424,a2m:[6,91],a_0:[239,320,369],a_0_real:239,a_1:320,a_2:320,a_3:320,a_4:320,a_c:377,a_cc:377,a_f:444,a_i:445,a_ij:369,a_j:445,a_pi:369,a_sigma:369,a_ss:377,aacut:275,aat:172,aatom1:115,aatom2:115,aatom3:115,ab_23_cd:333,abbrevi:12,abc:[3,12,333,456,484],abf:216,abf_integr:13,abi:192,abil:[3,9,215,252,280,293,387],abl:[3,8,11,12,39,86,188,192,214,223,227,316,323,363,456,484,487],ablat:320,about:[0,1,3,4,6,8,9,10,11,12,13,17,39,41,42,61,63,78,108,115,116,118,159,165,188,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,224,225,226,227,228,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,248,251,256,259,260,261,262,263,264,265,266,267,268,273,274,275,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,293,294,295,296,305,306,308,309,311,312,313,314,315,316,317,318,319,320,322,323,324,325,327,328,329,330,331,346,349,355,356,358,363,368,374,379,394,419,423,450,456,459,460,465,466,468,473,477,484,486,488],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,63,64,68,70,71,72,73,76,77,86,87,89,90,91,93,94,96,97,112,114,116,118,140,141,143,144,145,146,147,148,151,152,153,154,155,157,158,159,163,164,165,167,168,171,172,173,174,175,176,177,178,179,180,182,183,185,188,189,190,191,194,195,196,197,198,203,204,206,207,208,209,211,214,215,217,218,223,226,228,232,234,236,237,238,242,251,252,256,276,279,281,286,292,293,297,305,308,311,312,313,314,331,333,334,335,336,337,338,339,340,342,344,349,351,353,357,358,362,363,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,417,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283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,416,420,422,423,430,440,442,443,444,447,453,455,457,458,459,460,461,463,464,466,468,470,472,475,476,479,483,484,485,486,487,488],afterrun:466,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,453,455,456,458,460,465,472,474,484,486],against:[11,12,13,64,218,358,422,423],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,453,485],aggress:[232,472],agilio:[9,13],agre:[3,8,185,356,365,396,423],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,423],al2o3_001:[118,294],al3:164,ala:239,alain:9,alat:[274,410],alb:[420,442,444],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:420,alderton:382,alejandr:[252,253],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,427,429,453,455,472],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,458,461,479],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,453,455,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,475,476,477,479,483,484,485,486,487,488],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,418,423,458,466],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,414,420,423,424,427,429,438,448,450,453,456,458,460,461,462,463,464,465,468,470,471,472,475,476,484,485],almost:[2,3,12,60,234,283,320,349,360,363,438],alo:379,alon:[6,7,214,289,422,423,456],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,422,423,441,458,461,468,469,484],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,415,419,443,445,476,479],alpha_:445,alpha_c:407,alpha_i:[430,445],alpha_ialpha_j:445,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,439,458],alphanumer:[3,63,194,282,290,333,357,484],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,438,448,451,454,458,459,463,468,484],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,269,270,271,272,274,275,276,278,279,280,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,301,302,305,306,308,311,312,313,314,315,319,320,321,322,324,326,329,331,333,335,340,343,346,348,349,351,352,3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,363,365,369,379,380,410,414,426,428,444,462,468,479,481],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,424,438,448],cloud:479,clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:458,cmatrix:230,cmax:410,cmd:[11,12,276,469],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,462],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,425,470],coarser:[349,484],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,414,427,429,431,458,460],coeffcient:458,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,453],colberg:189,cold:[6,150,228,232,359,479],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,458,465,471,477,488],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,451],colllis:308,colloid:[],colombo:39,colon:[192,331,459],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,422,423,459,473,475,484],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,460],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,430,440,442,444,447,450,461,466,471,479,484],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,414,419,441],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,416,423,430,440,441,442,443,444,447,455,456,458,479,484],commerci:7,commmand:[3,6,12,59,107,271,452,453,455,472,487],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,430,442,444,458,461,470],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,418,455,456,460,467,468,484,486,488],communc:348,comp:[7,189,235,236,296,349,358,387,414,419,424,437,441,443],compact:[63,194,376,439],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,453,472,473,479,483],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,439],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,414,441,455,456,484],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,458,459,463,484],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,427,429,446,453,458,463,466,470,472,475,479,484],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,441,456,458,461,484],compli:[315,319],complic:[6,7,9,12,13,201,228,456],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,427,429,430,458,459,468,476,484,485],componenet:6,composit:[6,201,239,385],compound:[378,387,388,447],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,424,446],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:479,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,487],concav:329,concentr:385,concept:[6,145,155,203,467],conceptu:[3,6,71,153,215,217,358,379,394,410,463],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,484],conden:[320,442,444],condens:[6,147,320,365,381,385,399,447],condit:[],conducit:6,conduct:[],cone:461,confid:[3,472],config:[12,188,455],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,440,442,444,447,453,458,460,461,472],confin:[458,472],conflict:[3,12,40,414,456],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,470],confus:[3,447],conjuct:383,conjug:[7,8,236,355,387,422,423],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,414,417,425,445,458,461,465,479,488],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,438,444,455,456,462,479],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,453,459,461],consequ:[1,6,201,320,398,472],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,467,472],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,423,424,438,453,454,456,459,460,461,463,466,468,476,479,484],consider:[6,8,236,237,311,312,313,363,467],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,414,424,427,429,441,448,456,458,459,461,462,463,470,479,484],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,424],constitut:[427,429],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,463,470,479],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,414,438,440,441,461,462,477,484],constructor:8,consult:423,consum:[1,288,418,484],consumpt:346,contact:[],contact_stiff:[426,428],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,416,420,421,422,423,430,440,441,442,443,444,445,447,453,454,455,456,458,459,460,461,463,465,467,470,472,475,476,479,484,486,488],content:[12,18,423,474,476],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,450,458,465,474,483,484,485],contibut:70,contigu:455,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,422,423,424,427,429,443,453,456,458,460,461,466,472,475,476,484,486],continuum:[6,7,9,200,320,427,429],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,427,429,450,487],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,414,422,423,470,476,479],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,422,423,426,428,440,444,453,455,467,473,474],control_typ:200,controlfil:423,convect:91,conveni:[6,12,29,188,192,209,294,351,430,484],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,484],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,453,465,472],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,417,456,472,483],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,442,444,451,456,458,459,460,465,475,479,483,484,486,488],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,453,458,459,461,463,466,468,472,479,484,485],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,422,456],copper:451,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,471],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,470],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,446,458],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,449,450,451,458,473,476,479],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,455,456,458,468,483,485],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,419,420,422,423,424,425,430,431,440,441,442,443,444,446,447,449,450,451,453,455,456,458,459,461,471,472,473,475,476,479,484],correspondingli:[408,409,467],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,414,440,455,467],costheta0:[440,442,444,447],costheta:420,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,422,423,454,455,456,458,460,462,465,466,474,479,484,485],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,414,417,422,423,425,439,444,445,447,450,463,470,476,479,483],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,414,476,484],counter:[326,453,464,466,472],counteract:228,counterbal:232,counterpart:[188,293,453],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,431,455,458,471,479,484,486],courtesi:351,coval:[6,29,387,410,479],covari:230,cover:[6,71,185,191,200,239,387,397,446],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,439,453,471,472,475,476,477,484],cpuremain:476,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,479],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,419,446,460,463,484],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,463,472,473],criterioni:472,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,420,425,427,429,442,444,451,458,462,468,486],crossov:1,crossterm:458,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,462,476,479],crystallin:[6,275,351,443,479],crystallis:315,crystallogr:[118,164],crystallograph:[351,476],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,458],cs_re:[40,458],csanyi:[140,421,430],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,440,442,444,447],csinfo:6,csisi:[386,440,442,444,447],csld:[],cst:385,cstherm:6,cstyle:455,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,479],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,476],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,414,420,422,423,426,427,428,429,431,442,444,445,448,453,454,455,456,458,459,460,461,462,464,465,466,468,470,472,473,475,476,484,485,486,487,488],curv:[6,165,228,275],curvatur:[390,424,451],custom:[],cut0:456,cut1:467,cut2:467,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:420,cutoff1:[375,382,399,403,407,417,425],cutoff2:[370,372,373,375,381,382,399,403,407,417,425],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,456,460,463,467,479,484],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,484],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,461],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,468],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,417,425,439,445,472,479],damp_com:237,damp_drud:237,dampen:[293,479],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,476],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,475],dat:[6,91,185,200,454],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,422,423,484],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,442,444],daw:[385,420],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,459,463],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,414,448,456,457,460,465,468,475,484],deby:[],decai:[379,451],decid:[3,6,12,16,71,249,282,293,321,473],decipher:351,declar:189,declin:308,decod:190,decompos:[87,430],decomposit:[3,5,7,18,62,200,276],decoupl:[6,479],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,456],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,458,459,461,462,463,464,467,468,469,470,472,473,475,476,479,480,481,482,483,484,485],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,420,427,429,430,446,456,458,460,467,469,483,484],defint:476,deform:[],deg2theta:164,deg:479,degener:[3,278],degrad:[8,18,275,349,467],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,468,476,479,485],degress:[145,203],del:472,delai:[3,6,12,359,384,476],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,414,458,459,461,469,470,475,480,482,484,485],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[456,484],deloc:[253,387],delr:410,delt_lo:472,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,420],delta_mu:3,delta_pi:369,delta_r:420,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,423,427,429],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,420,424,433,435,436,437,458,467,468,476,483],density_continu:429,density_summ:429,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,419,420,422,423,424,425,430,431,439,440,441,442,443,444,445,446,447,449,450,451,453,455,458,460,461,464,468,470,472,475,476,478,484,485],dependend:6,depflag:12,dephas:[453,472],depos:218,deposit:[],deprec:[284,422],depth:[51,144,190,320,390,424],dequidt:9,der:[87,107,377,378,407,422,423,450,479],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,422,423,439,441,450,479],derjagin:450,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,419,420,421,422,423,424,425,430,431,438,439,440,441,442,443,444,445,447,449,450,451,453,455,456,458,459,461,462,468,471,472,475,484,485,486],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,420,423,441,467],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,440,442,444,454,455,456,458,462,467,472,473,475,476,484,485,486],desk:7,desktop:[4,6,7,10,12,190],despit:479,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,413,414,419,422,423,424,430,431,439,446,449,450,456,458,459,460,461,463,464,467,468,470,473,476,477,484,485,488],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,453,455,458,469,472,484],determ:363,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,414,423,424,438,441,445,450,455,458,459,461,463,465,468,472,474,475,477,483,484,485],detil:108,devan:[9,425],devanathan:444,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,447,460],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:479,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,427,429],diagonalstyl:430,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,424,446,450,458,459,468],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,414,442,444,466],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,413,414,416,420,422,423,424,425,426,427,429,430,431,439,440,441,442,444,446,447,450,452,453,455,456,458,460,461,462,463,466,467,468,470,472,473,475,476,477,479,483,484,485,486],differenti:[1,3,6,29,185,348,379,420,443],difficult:[215,276,363,393,467],difficulti:[296,422],diffract:[],diffus:[],digit:[2,3,191,333],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,461,483,484,485],dimdim:484,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,420,458,468],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,430,450],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,479],dir1:469,dir2:469,dir:[1,3,4,8,9,11,12,250,274,283,307,420,422,423,456,469,484],dirac:140,direc:420,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,414,417,425,438,456,468,469,470,476,484],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,416,420,421,422,423,430,440,442,443,444,447,456,458,459,460,469,484],disabl:[3,12,16,320,398,456,471,484],disadvantag:[6,211],disallow:[188,217,252],disappear:460,discard:[2,3,41,71,205,207,211,321,329,455,460,461],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,456],disloc:70,disord:[39,70],disp:[],dispar:424,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,414,423,441,447],displac:[],displace_atom:[],displace_box:59,displacemet:461,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,439],dispters:3,dissip:[6,229,236,275,317,318,371,383,391,408,409,439],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,438,453,485],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,38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229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,422,423,424,425,430,431,432,433,438,439,440,441,442,443,444,446,447,448,449,450,451,453,456,458,463,467,468,470,472,474,475,476,479,483,484,487],energy_update_freq:423,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,455,484,485],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[422,423],enhanc:[196,200,453],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,418,458,462,463],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,440,447],enter:[57,155,388,447,472],enthalpi:[123,254,255,385,475,476,484],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,414,441,458,466,467],entireti:[397,446],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,416,423,430,440,441,442,443,444,447,484],entropi:472,entry1:[38,56,191,376,441],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,420,442,455,469,484],epair:[107,191,389,393,422,423,476],epen:[422,423],epfl:[230,235],epp:382,epq:382,eps0:450,eps14:407,epsilon0:444,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,413,417,424,425,434,440,446,449,450,467,479,483],epsilon_0:451,epsilon_14:374,epsilon_:424,epsilon_d:380,epsilon_i:[390,414,424],epsilon_i_:424,epsilon_i_a:[390,424],epsilon_i_b:[390,424],epsilon_i_c:[390,424],epsilon_ij:414,epsilon_j:[390,414,424],epsilon_j_:424,epsilon_j_a:[390,424],epsilon_j_b:[390,424],epsilon_j_c:[390,424],epsilon_lj:424,epton:419,eqch:160,eqeq:[422,423],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,420,422,423,424,426,427,428,430,431,441,446,447,451,454,455,456,458,460,461,465,466,469,472,474,476,484,485],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,414,424,427,429,433,434,436,437,445,451,479],equi:253,equidist:251,equil:[3,284,352,465,488],equilater:468,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,422,423,454,468],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,416,479],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,442,444,458,461,466,467,476,479],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,458],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,414],erforc:113,erg:483,erhart:[201,385,442,444],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[442,444],erratum:325,erron:3,error:[],erta:391,ervel:[113,458],escap:[218,479],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,455],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,444,463,476],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,414,423,441,472,476],esu:483,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,420,443,447,483],eta_dot:252,eta_ij:420,eta_ji:388,etag:[40,458],etail:476,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,418,422,423,440,442,444,447,453,456,458,459,460,465,467,468,472,474,475,476,477,479,483,484,486,488],ethernet:18,etol:[356,358,453,472],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,475,476],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:432,europhi:239,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,414,420,426,428,441,453,454,456,460,461,463,465,466,467,468,472,474,476,484,485],evalut:[333,456],evan:[153,270],evanseck:[6,20,171,374,470],evapor:[],evaul:[8,356],evdwl:[107,422,423,476],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,414,424,447,448,458,459,461,463,464,465,467,468,470,473,475,476,477,479,488],evenli:[3,41,141,185,211,239,397,448,458],event:[],eventu:[3,6,12,15,167,284,472],ever:[54,56,235,308],evera:[377,390,424,439],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,422,423,435,452,453,454,458,460,462,463,465,466,467,472,473,474,476,484,488],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,453],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,417,425,439,441,460],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,460,465,472,484,486,488],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,414,441,460,461,468,472,484],exager:479,examin:[6,8,9,17,214,275],examp:[456,484],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,458,484],exceed:[3,41,59,211,217,252,308,466],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,419,422,423,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,455,456,458,460,461,463,466,467,468,469,470,472,476,479,483,484,485,487],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,473],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,414,438,470],exclus:[1,3,9,12,16,87,363,378,414,467,477],excurs:453,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,454,456,466,469,472,484],exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,484],exhibit:[252,355,387,467],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,422,448,454,456,458,459,460,469,470,471,484,485,486],exit:[2,3,11,12,41,57,188,211,347,362,456,457,466,475,484],exlanatori:3,exp:[],expand:[],expans:[12,140,188,469,484],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,414,453,456,458,460,463,467,472,484],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,456],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,414,467,472],experienc:[6,12,241,242],experiment:[228,348,363,472],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,446,456,459,460,463,465,468,479,484,488],explan:[3,6,59,113,140,188,203,251,274,394,452,455,456,458,467],explanatori:[3,8,117,188,202,203,206,207,208,293,357,455,484],explantori:[3,289],explic:413,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,445,452,455,459,462],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,414,415,416,417,419,424,425,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,447,449,450,451,458,460,467,468,470,471,477,479],explictli:[16,471],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,413,425],exponenti:[87,420,440,447,451,472,484],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,430,439,484],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,423,424,430,475,476],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,426,428,441,455,458,461],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,414,455,456,458,461,470,479,484],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,430,456,463,475],extract_atom:11,extract_comput:[11,456],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,443,479],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[442,443,444],f_ave:117,f_c:443,f_f:444,f_fix_id:283,f_harm:318,f_i:420,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,476,484],f_ij:420,f_indent:209,f_int:317,f_jj:91,f_k:420,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,442,443,444],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,424,458,461],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,470],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,414,416,417,423,425,431,440,445,455,458,461,462,467,470,472,473,476,479,483,484],factori:[3,456],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,423,456],failur:[121,427,457,484],fairli:[11,414,467,472],faken:73,falcon:233,fall:[3,6,191,206,279,456,484],fals:[86,331,333,484],fame:8,famili:[447,455],familiar:[0,11],fan:420,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,446,456,458,463,476],farago:236,farrel:[442,444],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,461,470,484,487],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,439,441,460,465,467,476,485,488],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,415,416,417,419,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,467,471,479],fastest:[1,6,14,17,153,207,320,321,363,455],fatal:[3,475],fault:[70,423],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,484],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,414],felling:412,felt:329,femtosecond:483,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,470],fermi:[1,12,15,151,363,444],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,455,458,463,467,469,477,484,486],fewer:[1,3,11,15,16,61,242,467],fewest:3,fextern:226,feynman:276,fff:456,ffield:[378,388,422,423],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,467],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,477],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:438,fictiti:[6,197,198,223,226,230,276,292,379,399,403,438],field1:[459,463],field2:459,field:[],fifth:[305,416],figur:[1,3,8,11,12,283,455,456],fij:382,file0:274,file1:[11,13,274,319,333,357,463,465,469],file2:[11,13,319,333,357,463,465,469],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,416,420,421,422,423,430,440,441,442,443,444,447,454,455,456,459,460,465,469,476,484,486,487,488],filennam:465,filep:[3,188,191,460,465,488],filepo:290,fill:[7,165,190,279,320,351,359,369,423,461],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,439,441,479,484],find_custom:8,fine:[16,17,169,197,223,318,359,363,484],finer:[140,165,484],finest:348,finger:[165,187,249,461],finish:[6,11,41,211,333,345,347,348,360,362,363,446,463,484,485],finit:[],finni:[7,385,439],finvers:221,fiorin:[9,216],fire:[354,355,356,358,472],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,414,416,420,422,423,430,438,440,441,442,443,444,447,451,453,454,455,456,458,459,460,463,465,467,470,471,472,475,476,479,484,485,486,488],fischer:[6,9,19,20,171,374,470],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,414,434,441,443,466,484],five:[73,151,283,357,369,411,458,472],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:422,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,438,453,455,456,458,459,460,462,463,464,468,484],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,443,476],flip:[3,6,217,252,327,328],floor:484,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,475],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,476,479],fmackai:9,fmag:219,fmass:276,fmax:[356,476],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,467,478,483,485],fname:347,fno:[12,16],fnorm:[356,476],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,423],foil:[140,274,430],fold:[306,467],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,456,458,459,460,461,463,465,466,467,470,472,473,474,479,484,485,487],foo:[4,8,11,12,188,1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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,414,422,423,438,439,453,454,455,458,459,461,463,465,466,467,470,472,474,475,476,477,478,483,485,486,487],"function":484,"long":[205,370,372,373,374,375,379,381,382,399,403,407,417,425],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,484],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,450],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,484],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,417,425],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,415,440,442],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,413,417],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],diagnost:7,diel:380,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,382],direct:221,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:383,drag:219,dreid:[6,393],drude:[6,9,150,220,221,237],dsf:[379,399],dsmc:384,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:284,eam:[13,385],echo:193,edip:386,eff:[9,13,96,97,149,151,156,238,253,263,271,314,387],efield:223,eim:388,elast:6,emac:13,enforce2d:224,ensembl:7,erot:[82,83,84,85],error:3,evapor:225,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],exp:[27,174],expand:[46,402],extend:[8,11],extern:226,fcc:274,featur:[7,8,484],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,484],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,27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,449,450,451],pair_writ:448,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:452,past:5,per:6,perform:[1,10],peri:419,period:25,phonon:[9,13,275],pimd:276,piston:327,planeforc:277,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:419,poem:[9,278],point:284,polariz:6,poli:[371,408,409],polym:13,polymorph:420,post:7,potenti:[2,6,8],pour:279,pppm:6,prd:453,pre:7,press:280,pressur:112,previou:12,print:[281,454],problem:[3,4],process:[6,7],processor:455,profil:153,properti:[6,113,114,115,282],pymol_aspher:13,python:[9,11,13,456],qbmsst:283,qeq:[284,285,286],qmmm:[9,287],qtb:[9,288],quadrat:183,quantiti:6,quartic:[35,54],quip:421,quit:457,ramp:154,rattl:296,rdf:116,read_data:458,read_dump:459,read_restart:460,reax:[9,13,286,289,290,422,423],reaxc:9,rebo:365,recent:291,reduc:117,refer:484,reflect:328,region:[8,117,155,156,329,461,484],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,227,228,229,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,293,294,295,297,298,299,300,301,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,347,348,349,351,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,470,471,472,473,474,475,476,477,478,480,481,482,484,485,486,487,488],relax:215,replic:462,replica:[6,7],report:3,requir:12,rerun:463,rescal:[313,314],reset:222,reset_timestep:464,resquar:424,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,465],restrain:292,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],rho:126,rhosum:435,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,466],run_styl:467,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,425],self:307,serial:11,set:[6,468],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,469],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,426,427,428,429],smooth:[405,406],sna:140,snad:140,snap:430,snapshot:6,snav:140,soft:[407,431],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,414,484],special_bond:470,sph:[9,432,433,434,435,436,437],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:438,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:471,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],system:6,tabl:[0,6,38,56,185,441,442],tad:472,taitwat:[436,437],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:473,temperatur:6,tersoff:[442,443,444],test:11,tfmc:315,thermal:[6,316],thermo:[6,474],thermo_modifi:475,thermo_styl:476,thermodynam:[6,8],thermostat:6,thole:445,time:[6,209],timer:477,timestep:478,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:427,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:160,transform:221,tri:[268,446],tri_surfac:428,triangle_mesh_vertic:134,tric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\ No newline at end of file
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:[16,245,282,320,391,424],cart:[3,457],carter:[9,17],cartesian:[3,62,364,457],carv:168,cascad:[222,320],cash:7,cast:[230,486],cat:[15,190],catastroph:284,cate:239,categori:[],cation:[388,431],cauchi:[133,138],caus:[1,2,3,6,8,12,16,17,165,167,168,169,188,191,199,215,222,228,264,274,291,293,296,325,327,328,329,330,333,347,349,356,358,362,393,399,405,408,409,415,454,458,459,460,461,464,465,467,468,486,490],caution:[1,349],cautiou:[212,213],cautious:365,caveat:[365,469],cbecker:[364,385],cc1:[6,14,66,75,90,93,104,106,114,145,160,162,203,207],cc2:14,ccc:[386,442,444,446,449],ccflag:[12,16,17,18,19,188],ccm6:385,ccsi:[386,442,444,446,449],ccu:369,cd2:164,cdeam:385,cdennist:9,cdll:11,cdof:[6,145,203],cdte:369,cdte_bop:369,cdtese:369,cdzn:369,cdznte:369,ce3:164,ce4:164,ceas:355,ceil:486,cell:[3,6,59,88,116,118,163,164,165,188,199,215,216,228,233,250,252,253,256,275,283,286,320,348,349,351,384,387,413,478],cella:[6,478],cellalpha:[6,478],cellb:[6,478],cellbeta:[6,478],cellc:[6,478],cellgamma:[6,478],center:[3,6,25,42,63,66,71,74,75,86,89,90,98,103,104,105,114,116,118,145,146,147,150,153,157,160,162,165,190,191,194,195,196,198,203,206,207,208,215,217,218,219,221,228,229,234,236,237,242,248,252,257,258,269,270,272,275,279,284,290,291,293,294,297,305,306,308,310,311,312,313,315,316,318,325,329,334,351,357,368,386,387,390,391,397,408,409,410,411,412,442,444,445,446,448,449,463,470,481,486],centimet:485,central:[3,61,70,76,77,116,122,140,242,274,296,306,357,413,417,423,424,449,460],centro:[],centroid:[3,276,448,470],cerda:348,ceriotti2:230,ceriotti:[13,230,235],certain:[1,2,3,6,8,12,17,39,71,113,117,119,169,188,190,202,203,204,206,207,208,209,214,226,227,293,295,309,322,333,340,347,359,394,415,424,447,462,466,481,486],certainli:234,cerutti:349,cfg:[3,6,7,13,188,189,190,191,192],cfile:424,cfl:[128,298],cfor:297,cg_type:426,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:296,ch2lmp:[],ch3:296,ch5md:189,chain3:359,chain:[],challeng:[6,297],chalopin:288,champaign:[233,348,349,408],chan:413,chandler:[364,385],chandrasekhar:[6,399],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,147,148,149,165,166,167,169,185,187,188,189,190,191,192,194,195,196,197,198,200,201,207,208,210,211,212,213,214,215,216,217,218,222,223,225,227,228,230,232,233,234,236,238,239,240,242,248,249,250,252,253,254,255,256,257,258,264,269,270,271,272,274,275,279,280,282,283,287,290,291,292,293,295,296,297,308,311,312,313,314,316,317,318,319,320,321,323,326,329,331,349,354,356,358,361,363,383,387,391,394,408,409,410,413,415,423,424,431,441,455,456,457,458,460,461,462,463,464,465,466,468,469,470,471,472,475,478,482,484,485,486,487,488],change_box:[],changeabl:188,channel:[4,197],chapter:[276,349],charact:[2,3,6,12,38,41,56,63,185,188,190,191,192,194,211,282,290,333,357,362,387,398,421,423,424,431,443,457,458,462,467,468,486,488,489,490],character:[6,67,70,116,140,432,455,474],characterist:[237,308,317],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,164,165,188,192,194,195,196,201,218,223,228,282,284,285,286,290,310,323,348,349,357,370,372,378,379,381,382,385,387,388,394,399,403,407,418,423,424,431,441,446,447,449,450,452,453,460,461,465,470,472,481,485,486],charmm2lammp:13,charmm:[],chartreus:191,cheap:308,cheaper:[222,390,425],check:[3,6,8,11,12,15,17,39,41,71,91,185,201,207,211,212,213,218,225,228,234,235,292,296,308,316,318,323,331,333,347,356,357,358,359,360,363,384,395,398,415,424,455,457,458,460,468,474,477,478,486],checkf:185,checkqeq:424,checku:185,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,171,172,182,205,216,221,229,230,237,239,251,252,253,270,271,276,280,283,285,293,297,308,311,312,315,316,317,318,325,334,342,344,348,349,355,358,365,370,374,375,378,379,380,382,383,387,389,390,392,393,399,403,404,407,410,414,415,418,431,440,447,469,472,474,481],chemic:[9,118,159,164,188,200,201,228,284,289,290,315,349,423,424,436],chemistri:[9,283,284,286,369,387,423,424],chen:320,cheng:378,chenoweth:[423,424],chenoweth_2008:[423,424],chi:[92,154,187,274,284,286,388,390,487],chiefli:422,child:8,chip:[7,12,17,18,363,473],chipot:216,chiral:342,chmod:[11,12],cho:410,chocol:[7,191],choic:[3,6,12,15,16,18,40,41,54,87,141,144,158,169,185,203,207,208,211,214,217,218,230,236,239,250,252,276,284,293,315,343,349,354,355,358,360,363,394,407,415,419,460,469,470,473,474,480,481,485],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,155,156,190,212,213,214,215,218,225,236,239,250,252,254,255,256,257,258,280,308,312,326,348,349,355,450,455,457,469,475],chose:[444,446],chosen:[2,3,6,12,17,140,165,168,177,185,190,196,201,215,218,225,228,229,237,239,250,252,256,276,279,290,308,312,315,316,321,323,324,330,349,350,355,363,387,391,397,398,401,426,444,455,469,474,481],chri:163,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,145,160,162,203],chute:[4,10,231],ciccotti:296,cieplak:[6,171,472],cii:204,cij:204,circl:304,circular:[3,6,144,186],circumst:18,circumv:288,citat:[],cite:[3,7,8,12,236,431],cko:2,cl1:164,clarendon:[29,382],clarifi:[7,444,446],clariti:333,clark:418,class2:[],classic:[0,3,5,6,7,8,9,226,276,283,288,320,344,387],classifi:[9,441,449],claus:458,clean:[6,12,14,15,17,468],cleanli:[459,489],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:464,click:[2,11,22,37,44,55,165,173,184,190,233,335,343,358,376,441],client:[233,235],climb:[251,358,474],clinic:[7,13],clo:[154,187,487],clock:[12,455,474],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,446,464,470,481,483],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,440,450],cloud:[431,481],clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:460,cmatrix:230,cmax:410,cmd:[11,12,276,471],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,464],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,472],coarser:[349,486],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,433,460,462],coeffcient:460,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,455],colberg:189,cold:[6,150,228,232,359,481],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,460,467,473,479,490],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,453],colllis:308,colloid:[],colombo:39,colon:[192,331,461],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,461,475,477,486],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,462],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,432,442,444,446,449,452,463,468,473,481,486],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,443],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,432,442,443,444,445,446,449,457,458,460,481,486],commerci:7,commmand:[3,6,12,59,107,271,454,455,457,474,489],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,432,444,446,460,463,472],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,457,458,462,469,470,486,488,490],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,439,443,445],compact:[63,194,376,441],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,431,455,474,475,481,485],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,441],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,443,457,458,486],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,460,461,465,486],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,448,455,460,465,468,472,474,477,481,486],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,443,458,460,463,486],compli:[315,319],complic:[6,7,9,12,13,201,228,458],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,432,460,461,470,478,486,487],componenet:6,composit:[6,201,239,385],compound:[378,387,388,449],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,448],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:481,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,489],concav:329,concentr:385,concept:[6,145,155,203,469],conceptu:[3,6,71,153,215,217,358,379,394,410,465],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,486],conden:[320,444,446],condens:[6,147,320,365,381,385,399,449],condit:[],conducit:6,conduct:[],cone:463,confer:413,confid:[3,474],config:[12,188,457],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,442,444,446,449,455,460,462,463,474],confin:[460,474],conflict:[3,12,40,415,458],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,472],confus:[3,449],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,447,460,463,467,481,490],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,440,446,457,458,464,481],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,455,461,463],consequ:[1,6,201,320,398,474],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,431,469,474],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,431,440,455,456,458,461,462,463,465,468,470,478,481,486],consider:[6,8,236,237,311,312,313,363,469],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,431,443,450,458,460,461,463,464,465,472,481,486],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,465,472,481],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,440,442,443,463,464,479,486],constructor:8,consult:424,consum:[1,288,419,486],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,432,442,443,444,445,446,447,449,455,456,457,458,460,461,462,463,465,467,469,472,474,477,478,481,486,488,490],content:[12,18,424,476,478],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,452,460,467,476,485,486,487],contibut:70,contigu:457,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,445,455,458,460,462,463,468,474,477,478,486,488],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,452,489],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,431,472,478,481],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,442,446,455,457,469,475,476],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,432,486],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,486],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,431,455,467,474],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,458,474,485],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,444,446,453,458,460,461,462,467,477,481,485,486,488,490],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordb:431,coordbb:431,coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,431,455,460,461,463,465,468,470,474,481,486,487],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,458],copper:453,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,473],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,472],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,448,460],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,451,452,453,460,475,478,481],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,457,458,460,470,485,487],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,433,442,443,444,445,446,448,449,451,452,453,455,457,458,460,461,463,473,474,475,477,478,481,486],correspondingli:[408,409,469],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,442,457,469],costheta0:[442,444,446,449],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,456,457,458,460,462,464,467,468,476,481,486,487],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,431,441,446,447,449,452,465,472,478,481,485],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,478,486],counter:[326,455,466,468,474],counteract:228,counterbal:232,counterpart:[188,293,455],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,433,457,460,473,481,486,488],courtesi:351,cov:431,coval:[6,29,387,410,431,481],covari:230,cover:[6,71,185,191,200,239,387,397,448],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,441,455,473,474,477,478,479,486],cpuremain:478,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,481],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,448,462,465,486],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,431,465,474,475],criterioni:474,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,444,446,453,460,464,470,488],crossov:1,crossterm:460,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,464,478,481],crystallin:[6,275,351,445,481],crystallis:315,crystallogr:[118,164],crystallograph:[351,478],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,460],cs_re:[40,460],csanyi:[140,422,432],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,442,444,446,449],csinfo:6,csisi:[386,442,444,446,449],csld:[],cst:385,cstherm:6,cstyle:457,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,481],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,478],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,433,444,446,447,450,455,456,457,458,460,461,462,463,464,466,467,468,470,472,474,475,477,478,486,487,488,489,490],curv:[6,165,228,275],curvatur:[390,425,453],custom:[],cut0:458,cut1:469,cut2:469,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,458,462,465,469,481,486],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,486],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,463],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,470],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,441,447,474,481],damp_com:237,damp_drud:237,dampen:[293,481],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,478],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,477],dat:[6,91,185,200,456],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,486],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,444,446],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,461,465],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,450,458,459,462,467,470,477,486],deby:[],decai:[379,453],decid:[3,6,12,16,71,249,282,293,321,475],decipher:351,declar:189,declin:308,decod:190,decompos:[87,432],decomposit:[3,5,7,18,62,200,276],decoupl:[6,481],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,458],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,463,464,465,466,469,470,471,472,474,475,477,478,481,482,483,484,485,486,487],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,432,448,458,460,462,469,471,485,486],defint:478,deform:[],deg2theta:164,deg:481,degener:[3,278],degrad:[8,18,275,349,469],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,470,478,481,487],degress:[145,203],del:474,delai:[3,6,12,359,384,478],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,460,461,463,471,472,477,482,484,486,487],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[458,486],deloc:[253,387,431],delr:410,delt_lo:474,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,431,435,437,438,439,460,469,470,478,485],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,433,441,442,443,444,445,446,447,448,449,451,452,453,455,457,460,462,463,466,470,472,474,477,478,480,486,487],dependend:6,depflag:12,dephas:[455,474],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,452,481],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,441,443,452,481],derjagin:452,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,433,440,441,442,443,444,445,446,447,449,451,452,453,455,457,458,460,461,463,464,470,473,474,477,486,487,488],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,443,469],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,442,444,446,456,457,458,460,464,469,474,475,477,478,486,487,488],desk:7,desktop:[4,6,7,10,12,190],despit:481,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,433,441,448,451,452,458,460,461,462,463,465,466,469,470,472,475,478,479,486,487,490],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,455,457,460,471,474,486],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,431,440,443,447,452,457,460,461,463,465,467,470,474,476,477,479,485,486,487],detil:108,devan:[9,426],devanathan:446,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,431,449,462],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:481,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:432,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,448,452,460,461,470],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,444,446,468],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,433,441,442,443,444,446,448,449,452,454,455,457,458,460,462,463,464,465,468,469,470,472,474,475,477,478,479,481,485,486,487,488],differenti:[1,3,6,29,185,348,379,421,445],difficult:[215,276,363,393,469],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,463,485,486,487],dimdim:486,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,460,470],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,432,452],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,481],dir1:471,dir2:471,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,458,471,486],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,440,458,470,471,472,478,486],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,432,442,444,445,446,449,458,460,461,462,471,486],disabl:[3,12,16,320,398,458,473,486],disadvantag:[6,211],disallow:[188,217,252],disappear:462,discard:[2,3,41,71,205,207,211,321,329,457,462,463],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,458],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,443,449],displac:[],displace_atom:[],displace_box:59,displacemet:463,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,441],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,441],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,440,455,487],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,458,460,463,469,470,474,478,481,485,487],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,459],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,453,458],div:8,divd:117,diverg:[3,12,39,293,318,462,481,488],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,431,449,469,477,486],divis:[6,239,369,397,407,457,460,478,486],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,460,461,465],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:470,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,452],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,432,441,442,444,446,448,449,458,460,461,462,463,465,468,469,470,477,478,486,487,488,489],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,456,457,458,460,461,462,463,464,467,468,470,471,472,473,474,477,478,481,486,490],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,442,444,445,446,449,460,462],dof:[3,8,112,144,145,158,203,293,487],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,460],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,455,457,460,464,477],domin:[1,387,474],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,431,458,460],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,440,443,448,455,456,457,458,461,464,465,468,478,479,481,486,487],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,456,460,464,468,473,486,487],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,431,459,479],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,431,457],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,455],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237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113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,206,208,209,214,217,221,229,234,236,237,238,251,252,253,264,280,292,293,297,308,311,312,313,314,316,319,320,323,327,330,331,347,348,357,358,362,363,383,385,390,413,425,428,430,432,433,447,450,455,458,460,461,462,463,465,467,468,472,476,478,481,486,490],end_of_step:8,endbondtors:[3,172,178,460],endif:8,energet:[214,365,424],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,431,432,433,434,435,440,441,442,443,444,445,446,448,449,450,451,452,453,455,458,460,465,469,470,472,474,476,477,478,481,485,486,489],energy_compon:431,energy_update_freq:424,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,457,486,487],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[423,424],enhanc:[196,200,455],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,419,460,464,465],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,442,449],enter:[57,155,388,413,449,474],enthalpi:[123,254,255,385,477,478,486],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,415,443,460,468,469],entireti:[397,448],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,417,424,432,442,443,444,445,446,449,486],entropi:474,entry1:[38,56,191,376,443],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,421,444,457,471,486],epair:[107,191,389,393,423,424,478],epen:[423,424],epfl:[230,235],epp:382,epq:382,eps0:452,eps14:407,epsilon0:446,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,414,418,425,426,436,442,448,451,452,469,481,485],epsilon_0:453,epsilon_14:374,epsilon_:425,epsilon_d:380,epsilon_i:[390,415,425],epsilon_i_:425,epsilon_i_a:[390,425],epsilon_i_b:[390,425],epsilon_i_c:[390,425],epsilon_ij:415,epsilon_j:[390,415,425],epsilon_j_:425,epsilon_j_a:[390,425],epsilon_j_b:[390,425],epsilon_j_c:[390,425],epsilon_lj:425,epton:420,eqch:160,eqeq:[423,424],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,414,421,423,424,425,427,428,429,431,432,433,443,448,449,453,456,457,458,460,462,463,467,468,471,474,476,478,486,487],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,415,425,428,430,435,436,438,439,447,453,481],equi:253,equidist:251,equil:[3,284,352,467,490],equilater:470,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,423,424,456,470],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,417,431,481],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,431,444,446,460,463,468,469,478,481],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,460],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:485,erhart:[201,385,444,446],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[444,446],erratum:325,erron:3,error:[],erta:391,ervel:[113,460],escap:[218,481],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,457],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,446,465,478],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,443,474,478],esu:485,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,445,449,485],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,460],etail:478,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,413,419,423,424,442,444,446,449,455,458,460,461,462,467,469,470,474,476,477,478,479,481,485,486,488,490],ethernet:18,etol:[356,358,455,474],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,477,478],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:434,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,431,443,455,456,458,462,463,465,467,468,469,470,474,476,478,486,487],evalut:[333,458],evan:[153,270],evanseck:[6,20,171,374,472],evapor:[],evaul:[8,356],evdwl:[107,423,424,478],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,449,450,460,461,463,465,466,467,469,470,472,475,477,478,479,481,490],evenli:[3,41,141,185,211,239,397,450,460],event:[],eventu:[3,6,12,15,167,284,474],ever:[54,56,235,308],evera:[377,390,425,441],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,431,437,454,455,456,460,462,464,465,467,468,469,474,475,476,478,486,490],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,455],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,441,443,462],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,462,467,474,486,488,490],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,443,462,463,470,474,486],exager:481,examin:[6,8,9,17,214,275],examp:[458,486],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,460,486],exceed:[3,41,59,211,217,252,308,468],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,457,458,460,462,463,465,468,469,470,471,472,474,478,481,485,486,487,489],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,475],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,440,472],exclus:[1,3,9,12,16,87,363,378,413,415,469,479],excurs:455,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,456,458,468,471,474,486],exempl:431,exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,486],exhibit:[252,355,387,469],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,450,456,458,460,461,462,471,472,473,486,487,488],exit:[2,3,11,12,41,57,188,211,347,362,458,459,468,477,486],exlanatori:3,exp:[],expand:[],expans:[12,140,188,471,486],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,455,458,460,462,465,469,474,486],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,458],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,469,474],experienc:[6,12,241,242],experiment:[228,348,363,474],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,433,448,458,461,462,465,467,470,481,486,490],explan:[3,6,59,113,140,188,203,251,274,394,454,457,458,460,469],explanatori:[3,8,117,188,202,203,206,207,208,293,357,457,486],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,447,454,457,461,464],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,451,452,453,460,462,469,470,472,473,479,481],explictli:[16,473],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,442,449,453,474,486],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,432,441,486],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,432,477,478],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,443,457,460,463],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,457,458,460,463,472,481,486],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,432,458,465,477],extract_atom:11,extract_comput:[11,458],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,445,481],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[444,445,446],f_ave:117,f_c:445,f_f:446,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,478,486],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,444,445,446],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,460,463],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,431,472],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,433,442,447,457,460,463,464,469,472,474,475,478,481,485,486],factori:[3,458],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,458],failur:[121,428,459,486],fairli:[11,415,469,474],faken:73,falcon:233,fall:[3,6,191,206,279,458,486],fals:[86,331,333,431,486],fame:8,famili:[449,457],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,448,458,460,465,478],farago:236,farrel:[444,446],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,463,472,486,489],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,441,443,462,467,469,478,487,490],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,469,473,481],fastest:[1,6,14,17,153,207,320,321,363,457],fatal:[3,477],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,486],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:485,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,472],fermi:[1,12,15,151,363,446],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,431,457,460,465,469,471,479,486,488],fewer:[1,3,11,15,16,61,242,469],fewest:3,fextern:226,feynman:276,fff:458,ffield:[378,388,423,424,431],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,469],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,479],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:440,fictiti:[6,197,198,223,226,230,276,292,379,399,403,440],field1:[461,465],field2:461,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,457,458],fij:382,file0:274,file1:[11,13,274,319,333,357,465,467,471],file2:[11,13,319,333,357,465,467,471],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,432,442,443,444,445,446,449,456,457,458,461,462,467,471,478,486,488,489,490],filennam:467,filep:[3,188,191,462,467,490],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,463],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,431,441,443,481,486],find_custom:8,fine:[16,17,169,197,223,318,359,363,486],finer:[140,165,486],finest:348,finger:[165,187,249,463],finish:[6,11,41,211,333,345,347,348,360,362,363,448,465,486,487],finit:[],finni:[7,385,441],finvers:221,fiorin:[9,216],fire:[354,355,356,358,474],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,432,440,442,443,444,445,446,449,453,455,456,457,458,460,461,462,465,467,469,472,473,474,477,478,481,486,487,488,490],fischer:[6,9,19,20,171,374,472],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,436,443,445,468,486],five:[73,151,283,357,369,411,460,474],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,413,440,455,457,458,460,461,462,464,465,466,470,486],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,445,478],flip:[3,6,217,252,327,328],floor:486,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,477],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,478,481],fmackai:9,fmag:219,fmass:276,fmax:[356,478],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,469,480,485,487],fname:347,fno:[12,16],fnorm:[356,478],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,432],fold:[306,469],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,420,421,422,423,424,425,426,428,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,457,458,460,461,462,463,465,467,468,469,472,474,475,476,481,486,487,489],foo:[4,8,11,12,188,190,226,458,471,486],foot:6,footprint:[12,363],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:242,forcefield:[292,393],forcegroup:239,forcezero:354,ford:382,forestgreen:191,forev:71,forget:[237,481],forgiv:252,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,213,229,230,236,238,242,249,270,275,286,288,292,293,320,325,329,334,335,342,353,355,357,358,365,366,369,376,385,387,389,393,394,398,410,412,413,417,418,421,423,424,425,431,432,433,441,443,444,445,446,452,454,457,458,460,465,470,477,481,486],formal:[6,78,80,91,229,230,236,252,276,308,316,431],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,206,207,208,209,211,213,275,278,282,284,286,289,293,294,304,319,320,331,332,335,353,357,358,364,365,369,376,385,388,398,410,412,422,423,424,426,432,443,449,450,457,458,460,461,462,465,476,477,478,486,488],former:[6,12,16,39,41,191,211,320,324,369,371,466,472,486],formerli:[7,13],formul:[1,40,64,141,197,223,236,252,270,284,286,292,296,319,348,365,369,385,387,390,410,420],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,164,165,170,172,173,184,188,195,196,197,198,203,204,205,206,209,210,217,223,231,232,234,236,237,249,274,275,281,290,295,302,306,308,311,312,313,322,325,328,330,331,333,334,335,337,343,351,357,365,366,368,369,374,375,376,377,382,383,385,386,390,391,392,393,395,398,399,401,402,403,405,406,408,409,410,414,415,416,425,426,433,441,442,444,445,446,449,451,452,456,460,463,470,477,478,485,486,487],forth:[1,6,11,12,13,14,15,362,458,463,467],fortran:[3,6,9,11,12,13,226,385,394,410,423,424],fortun:8,forward:[3,8,87,347,358,363],foster:[369,420,421],foul:168,found:[3,6,9,12,73,159,188,214,216,228,233,239,275,315,321,333,347,359,376,379,382,455,461,462,477],four:[6,11,54,81,103,104,140,161,250,320,342,357,358,413,455],fourier:[],fourth:[6,105,292,305,315,374,417,431],fox:[6,118,171,439,472],fphi:[38,56,443],fpic:12,fplo:[38,56,443],fprime:443,fqdn:235,fqq:382,frac:[221,237,447,481],fraction:[1,3,6,8,12,16,39,41,80,109,141,168,187,190,191,201,212,213,214,215,250,279,283,290,291,308,313,314,351,358,363,369,371,391,408,409,465,470],fragment:[42,233,290],frame:[83,140,191,200,250,283,327,390],framer:[190,191],framework:[5,230,364,432],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,159,196,274,308,317,318,319,320,355,358,366,387,407,413,421,452,457],freedom:[3,6,8,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,203,214,221,228,230,236,237,242,252,253,256,257,258,269,270,272,276,278,293,296,311,312,313,318,356,382,478,481,487],freeli:[0,6,7,12,144,158,163,190],freez:[],frenkel:[228,318],freq:199,frequenc:[3,6,16,39,191,205,264,275,276,283,288,346,383,387,424,431,455,469,474,486,489],frequent:[3,64,67,70,72,73,77,88,140,191,212,213,225,316,323,415,467],fri:[250,283],friction:[4,5,6,10,42,194,230,236,283,288,293,320,324,326,391,470],friedrich:298,from:[],front:[250,283,327],frontend:[190,287],frozen:[6,112,169,227,229,237,359,389],fs2:[6,91],fscale:233,fstr:486,fstring:458,ftol:[356,358,455,474],fuchsia:191,fuction:379,fudg:296,fugac:228,fugacity_coeff:228,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,190,204,205,216,239,274,348,349,363,369,385,387,388,390,447,460,462,467,468,472,474,479,481,489],full_energi:[3,228],fuller:356,fulli:[3,6,9,78,230,235,274,356,358,379,421,422,488],fulton:385,fumi:370,func:[458,486],funcfl:385,functino:[],functionaliri:216,fund:[0,7],fundament:[308,485],funnel_flow:304,funrol:413,further:[3,6,8,12,13,61,63,71,86,105,107,116,190,191,194,203,206,207,208,209,212,218,222,239,243,276,284,294,298,308,320,322,331,349,354,356,357,358,359,364,368,378,413,431,455,474,475,486],furthermor:[27,174,387],furthest:61,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g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ermut:[12,386,442,444,446,449],perpendicular:[6,144,190,217,234,244,249,251,274,277,301,325,326,355,460],perram:[349,390],persepct:190,persist:[3,8,71,226,293,363,457,458,466,486],person:9,persp:[3,190],perspect:190,pertain:[376,441],perturb:[9,13,70,87,248,291,325,328,330,465],peru:191,peskin:239,pessimist:349,petersen:[308,349],pettifor:[369,441],pettifor_1:369,pettifor_2:369,pettifor_3:369,pfactor:190,pforc:458,phantom:233,pharmaceut:7,phase:[3,12,16,252,315,323,369,399,445,457],phd:422,phenol:481,phenomena:387,phi0:[183,292],phi1:172,phi2:[172,386,442],phi3:[172,386,442],phi:[1,3,4,7,9,12,16,17,79,140,184,185,190,231,275,292,337,363,364,369,385,388,410,411,412,473],phi_ij:[369,388,421],philadelphia:9,phillip:[237,383,481],phillpot:[285,378,379,431],philosoph:385,philosophi:[6,7,235],phonon:[],phophor:432,phosphid:432,phy:[6,7,13,20,21,25,39,43,45,46,64,70,73,87,88,110,112,140,141,147,153,171,172,182,189,201,205,215,216,221,229,230,235,236,237,238,239,250,251,252,253,256,270,271,275,276,280,283,285,288,293,296,297,308,311,312,315,316,317,318,320,323,325,334,342,344,348,349,355,358,365,369,370,374,375,377,378,379,380,381,382,383,385,386,387,389,390,391,392,393,396,399,401,403,404,407,408,409,410,412,414,415,418,420,421,425,431,432,440,442,443,444,445,446,447,449,455,469,472,474,481],physic:[3,6,9,12,14,16,17,18,40,53,59,120,147,159,200,217,230,236,238,239,241,242,243,250,275,284,286,319,320,349,351,358,363,365,367,373,377,385,393,394,413,422,423,424,427,435,436,438,439,455,457,469,470,475,485],physica:[408,409],physik:[7,9],pic:9,picki:8,picocoulomb:485,picogram:485,picosecond:[191,217,478,485],picosend:387,pictur:7,piec:[3,11,140,191,252,467,490],pierr:9,pieter:13,pimd:[],pin:16,pink:191,pipe:[6,188,190],pipelin:[3,6],pisarev:320,pishevar:383,piston:[],pitera:6,pixel:190,pizza:[4,6,7,11,13,41,188,190,211],pjintv:13,pka:320,place:[3,6,7,9,11,12,33,41,50,71,87,159,165,169,178,185,188,190,191,193,194,195,196,213,214,217,228,229,230,232,235,236,237,238,240,242,243,252,257,258,269,272,279,282,291,293,311,312,313,320,325,328,330,347,376,393,441,448,457,458,461,468,470,478,486],placehold:[33,178,364,365,378,385,388,395,396,410,411,412,417,421,423,424,432,440,442,444,445,446,449],placement:[351,399],plai:[190,315],plain:[9,407,458],plan:[3,5,6,17,167,460],planar:[6,40,42,234,274,326,342,344],planck:[228,276],plane:[3,6,9,41,42,57,59,67,71,190,194,200,207,211,231,234,244,274,277,287,305,307,320,326,334,336,337,338,339,344,351,409,448,463,470],planeforc:[],plasma:[9,88,253,320,387],plastic:[],plastic_strain:121,plastic_strain_r:124,platform:[1,3,7,9,12,13,15,17,188,190,192,462,467,490],plath:[6,91,194,316,323],player:190,pleas:[0,3,7,11,12,13,200,230,239,243,275,278,289,315,331,386,388,420,428,430,431],plen:366,plimpton:[0,5,7,70,112,141,214,274,308,391,420],plo:29,plog:[3,12,469],ploop:[252,253,256],plot:[7,11,13,283,405,407,443,450],plu:[3,11,12,39,59,68,96,168,191,210,215,217,218,256,293,360,387],plug:9,plugin:[9,13,192,461],plum:191,pm3:164,pmb:[],pme:349,pmf:[216,297,305],png:[3,12,188,190],pni:190,poariz:6,poem:[],point1:460,point2:460,point3:460,point:[],point_data:294,pointer:[3,7,8,11,226,458],pois:485,poiseuil:[4,197,231],poisson:[59,217,349,391],poisson_solv:200,polak:355,polar:[6,7,140,147,164,200,220,378,379,399,447,481],polar_off:378,polar_on:378,polariz:[],poli:[],politano:[9,431],pollock:[7,349],polya:331,polybond:13,polychain:293,polydispers:[3,357,371,377,391,408,409,441,452],polygon:[6,163],polym:[],polymer:7,polymorph:[],polynomi:[9,38,56,185,385,405,415,431,436,443],polytechn:278,poor:[16,17,41,211,270,271,296,363,405],poorli:[355,356],pop:[3,8],popen:12,popul:[12,288,351,384,460],popular:[12,188,386],pore:305,poros:168,porou:[239,242],port:[233,235],portabl:[7,9,12,188,189,216,423,462],portion:[1,3,9,11,12,15,16,41,54,71,88,91,107,108,110,113,141,142,155,188,191,202,203,206,207,208,209,211,215,225,239,252,254,255,257,258,285,290,291,293,294,333,347,359,363,370,372,373,374,375,379,380,382,383,387,389,390,392,393,399,403,407,418,425,426,446,450,459,460,465,469,470,479,486],poschel:391,posfreq:290,posit:[3,6,14,27,39,40,41,42,46,57,59,70,71,81,89,90,103,104,108,117,118,122,140,141,148,163,164,165,167,168,169,174,176,185,187,189,190,191,194,195,197,199,201,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,228,229,230,231,233,234,236,237,238,239,241,242,245,246,249,250,252,253,254,255,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,283,284,288,290,291,293,296,297,301,304,305,307,308,310,311,312,313,315,317,318,319,320,323,325,326,327,328,329,330,331,334,348,351,358,365,366,368,371,383,384,387,389,397,402,424,431,440,443,448,455,460,463,470,481,486,487],posix:233,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,40,41,55,59,63,70,71,87,113,115,140,141,144,158,187,188,189,191,194,196,200,201,207,211,212,213,214,218,220,230,237,274,287,288,290,293,304,308,310,320,321,338,347,349,356,359,360,363,384,393,410,424,428,430,431,443,449,458,464,473,474,475,47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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,440,441,455,456,457,460,461,463,465,467,468,469,472,474,476,477,478,479,480,485,487,488,489],"function":486,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,486],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,452],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,486],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,442,444],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,7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66,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],rho:126,rhosum:437,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,468],run_styl:469,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,426],self:307,serial:11,set:[6,470],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,471],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,427,428,429,430],smooth:[405,406],smtbq:[9,431],sna:140,snad:140,snap:432,snapshot:6,snav:140,soft:[407,433],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,415,486],special_bond:472,sph:[9,434,435,436,437,438,439],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:440,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:473,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],system:6,tabl:[0,6,38,56,185,443,444],tad:474,taitwat:[438,439],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:475,temperatur:6,tersoff:[444,445,446],test:11,tfmc:315,thermal:[6,316],thermo:[6,476],thermo_modifi:477,thermo_styl:478,thermodynam:[6,8],thermostat:6,thole:447,time:[6,209],timer:479,timestep:480,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:428,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:160,transform:221,tri:[268,448],tri_surfac:429,triangle_mesh_vertic:134,triclin:6,tstat:383,ttm:320,tune:321,type:7,ulsph:430,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:344,uncomput:482,undump:483,unfix:484,unit:485,user:[9,12,14,16,18],vacf:161,valu:[6,486],variabl:[6,8,486],variou:1,vashishta:449,vcm:162,vector:[6,322,486],veloc:487,version:[0,5,12],via:12,vim:13,viscos:[6,323],viscou:[243,324],visual:6,vol:139,voronoi:[9,163],vtk:294,wall:[6,325,326,327,328,329,330],wall_surfac:304,warn:3,water:6,weight:206,what:[7,12],wolf:[370,379],wrapper:11,write:6,write_data:488,write_dump:489,write_restart:490,xmgrace:13,xmovi:13,xrd:164,xtc:9,yukawa:[451,452],zbl:[446,453]}})
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<title>temper command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="temper-command">
<span id="index-0"></span><h1>temper command<a class="headerlink" href="#temper-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>temper N M temp fix-ID seed1 seed2 index
</pre></div>
</div>
<ul class="simple">
<li>N = total # of timesteps to run</li>
<li>M = attempt a tempering swap every this many steps</li>
<li>temp = initial temperature for this ensemble</li>
<li>fix-ID = ID of the fix that will control temperature during the run</li>
<li>seed1 = random # seed used to decide on adjacent temperature to partner with</li>
<li>seed2 = random # seed for Boltzmann factor in Metropolis swap</li>
<li>index = which temperature (0 to N-1) I am simulating (optional)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.</p>
<p>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 6</span></a> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <a class="reference internal" href="Section_howto.html#howto-5"><span>this section</span></a> of the manual for further
discussion.</p>
<p>Each replica’s temperature is controlled at a different value by a fix
with <em>fix-ID</em> that controls temperature. Possible fix styles are
<a class="reference internal" href="fix_nh.html"><em>nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>temp/berendsen</em></a>,
<a class="reference internal" href="fix_langevin.html"><em>langevin</em></a> and <a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>.
The desired temperature is specified by <em>temp</em>, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the <a class="reference internal" href="variable.html"><em>variable</em></a>
command for more details. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt $t $t 100.0
+fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382
</pre></div>
</div>
<p>would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.</p>
<p>As the tempering simulation runs for <em>N</em> timesteps, a temperature swap
between adjacent ensembles will be attempted every <em>M</em> timesteps. If
<em>seed1</em> is 0, then the swap attempts will alternate between odd and
even pairings. If <em>seed1</em> is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
<em>seed2</em> in the random number generator.</p>
<p>As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the <a class="reference internal" href="Section_start.html#start-7"><span>section on command-line switches</span></a> for info on how to change these
names.</p>
<p>The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:</p>
<div class="highlight-python"><div class="highlight"><pre>Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
...
</pre></div>
</div>
<p>The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.</p>
<p>The last argument <em>index</em> in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The <em>index</em> value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the <em>N</em> values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:</p>
<div class="highlight-python"><div class="highlight"><pre>500000 2 4 0 1 3
</pre></div>
</div>
<p>then a setting of</p>
<div class="highlight-python"><div class="highlight"><pre>variable w world 2 4 0 1 3
</pre></div>
</div>
<p>would be used to restart the run with a tempering command like the
example above with $w as the last argument.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This command can only be used if LAMMPS was built with the REPLICA
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="variable.html"><em>variable</em></a>, <a class="reference internal" href="prd.html"><em>prd</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a></p>
<p><strong>Default:</strong> none</p>
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\ No newline at end of file
diff --git a/doc/temper.txt b/doc/temper.txt
index 6283c2b46..48c90cf90 100644
--- a/doc/temper.txt
+++ b/doc/temper.txt
@@ -1,132 +1,132 @@
"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
temper command :h3
[Syntax:]
temper N M temp fix-ID seed1 seed2 index :pre
N = total # of timesteps to run
M = attempt a tempering swap every this many steps
temp = initial temperature for this ensemble
fix-ID = ID of the fix that will control temperature during the run
seed1 = random # seed used to decide on adjacent temperature to partner with
seed2 = random # seed for Boltzmann factor in Metropolis swap
index = which temperature (0 to N-1) I am simulating (optional) :ul
[Examples:]
temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w :pre
[Description:]
Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "Section_start 6"_Section_start.html#start_7 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Possible fix styles are
"nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
"langevin"_fix_langevin.html and "temp/rescale"_fix_temp_rescale.html.
The desired temperature is specified by {temp}, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the "variable"_variable.html
command for more details. For example:
variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt $t $t 100.0
+fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382 :pre
would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.
As the tempering simulation runs for {N} timesteps, a temperature swap
between adjacent ensembles will be attempted every {M} timesteps. If
{seed1} is 0, then the swap attempts will alternate between odd and
even pairings. If {seed1} is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
{seed2} in the random number generator.
As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the "section on command-line
switches"_Section_start.html#start_7 for info on how to change these
names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
... :pre
The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
The last argument {index} in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The {index} value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the {N} values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:
500000 2 4 0 1 3 :pre
then a setting of
variable w world 2 4 0 1 3 :pre
would be used to restart the run with a tempering command like the
example above with $w as the last argument.
:line
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"variable"_variable.html, "prd"_prd.html, "neb"_neb.html
[Default:] none
diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.README b/examples/USER/mgpt/Ta6.8x.mgpt.README
new file mode 100644
index 000000000..5b26939ee
--- /dev/null
+++ b/examples/USER/mgpt/Ta6.8x.mgpt.README
@@ -0,0 +1,57 @@
+MGPT multi-ion potentials: Ta6.8x (Ta, version 6.8x)
+
+Author: John A. Moriarty
+
+Potential data files: Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin
+
+Volume mesh for potential data, with x = (vol/vol0)**(1/3):
+
+
+ x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0
+
+ 1.080 1.260 153.181 3.31924 13.237 0.794
+ 1.070 1.225 148.965 3.28851 13.612 0.816
+ 1.060 1.191 144.828 3.25777 14.001 0.840
+ 1.050 1.158 140.767 3.22704 14.405 0.864
+ 1.040 1.125 136.783 3.19631 14.824 0.889
+ 1.030 1.093 132.876 3.16557 15.260 0.915
+ 1.020 1.061 129.043 3.13484 15.714 0.942
+ 1.010 1.030 125.285 3.10410 16.185 0.971
+ 1.000 1.000 121.600 3.07337 16.675 1.000
+ 0.990 0.970 117.988 3.04264 17.186 1.031
+ 0.980 0.941 114.449 3.01190 17.717 1.062
+ 0.970 0.913 110.981 2.98117 18.271 1.096
+ 0.960 0.885 107.584 2.95044 18.848 1.130
+ 0.950 0.857 104.257 2.91970 19.449 1.166
+ 0.940 0.831 100.999 2.88897 20.077 1.204
+ 0.930 0.804 97.810 2.85824 20.731 1.243
+ 0.920 0.779 94.688 2.82750 21.415 1.284
+ 0.910 0.754 91.634 2.79677 22.128 1.327
+ 0.900 0.729 88.646 2.76603 22.874 1.372
+ 0.890 0.705 85.724 2.73530 23.654 1.419
+ 0.880 0.681 82.867 2.70457 24.470 1.467
+ 0.870 0.659 80.074 2.67383 25.323 1.519
+ 0.860 0.636 77.344 2.64310 26.217 1.572
+ 0.850 0.614 74.678 2.61237 27.153 1.628
+ 0.840 0.593 72.073 2.58163 28.134 1.687
+ 0.830 0.572 69.529 2.55090 29.164 1.749
+ 0.820 0.551 67.046 2.52016 30.244 1.814
+ 0.810 0.531 64.623 2.48943 31.378 1.882
+ 0.800 0.512 62.259 2.45870 32.569 1.953
+
+Corresponding T = 0 bcc pressure range: -30 GPa to 422 GPa
+
+
+General references to MGPT potentials:
+
+ J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994).
+
+ J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
+ P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
+
+
+Specific references to Ta6.8x potentials:
+
+ J. A. Moriarty and J. B. Haskins, Phys. Rev. B 90, 054113 (2014).
+
+ J. B. Haskins, J. A. Moriarty, and R. Q. Hood, Phys. Rev. B 86, 224104 (2012).
diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.parmin b/examples/USER/mgpt/Ta6.8x.mgpt.parmin
new file mode 100644
index 000000000..39517f112
--- /dev/null
+++ b/examples/USER/mgpt/Ta6.8x.mgpt.parmin
@@ -0,0 +1,2 @@
+ 0.80 1.08 0.01 121.60
+ 6.00 -4.00 1.00 0.00 2
diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.potin b/examples/USER/mgpt/Ta6.8x.mgpt.potin
new file mode 100644
index 000000000..9c014000a
--- /dev/null
+++ b/examples/USER/mgpt/Ta6.8x.mgpt.potin
@@ -0,0 +1,11253 @@
+# DATE: 2015-07-30 CONTRIBUTOR: John Moriarty moriarty2@llnl.gov CITATION: see Ta6.8x.mgpt.README in potentials directory
+ ta 0 4 0.00000
+ 2.00000E+00 1.53181E+02 3.31924E+00 1.80948E+02
+ 2.15000E+00 7.50000E+01 2.75000E+00 4.25000E+00
+ 3.80000E+00 1.00000E-05 -3.65805E-01 -2.92162E-03 -2.44225E-01
+ 3.11534E-04 3.79378E-02 -4.86257E-03 1.69740E-03 3.51980E-03
+ -2.94905E+01 9.66935E-01 1.08166E+01 6.76695E+00 1.99299E-01
+ 2.00000E+00 2.10000E+01 5.00000E-02
+ 2.00 2.213039E+01 -2.547846E+01 -6.481590E-03
+ 2.05 1.973742E+01 -2.176319E+01 -4.145906E-02
+ 2.10 1.764785E+01 -1.861644E+01 -6.467906E-02
+ 2.15 1.582293E+01 -1.596681E+01 -7.633587E-02
+ 2.20 1.420515E+01 -1.372091E+01 -7.701703E-02
+ 2.25 1.278212E+01 -1.183854E+01 -7.267747E-02
+ 2.30 1.153167E+01 -1.026808E+01 -6.453417E-02
+ 2.35 1.041815E+01 -8.931564E+00 -5.121229E-02
+ 2.40 9.422608E+00 -7.788314E+00 -4.042365E-02
+ 2.45 8.538842E+00 -6.826115E+00 -2.938902E-02
+ 2.50 7.749337E+00 -6.007072E+00 -1.821632E-02
+ 2.55 7.034189E+00 -5.287512E+00 -1.027560E-02
+ 2.60 6.393342E+00 -4.671745E+00 -3.570124E-03
+ 2.65 5.818116E+00 -4.143232E+00 1.799167E-03
+ 2.70 5.294678E+00 -3.673296E+00 5.529301E-03
+ 2.75 4.821908E+00 -3.263194E+00 7.672723E-03
+ 2.80 4.395243E+00 -2.906071E+00 8.403228E-03
+ 2.85 4.007620E+00 -2.589600E+00 9.310074E-03
+ 2.90 3.655310E+00 -2.308543E+00 8.862679E-03
+ 2.95 3.336307E+00 -2.061314E+00 7.736206E-03
+ 3.00 3.046749E+00 -1.842546E+00 6.934446E-03
+ 3.05 2.782658E+00 -1.646667E+00 5.638644E-03
+ 3.10 2.543024E+00 -1.473373E+00 4.255964E-03
+ 3.15 2.325510E+00 -1.320004E+00 2.987463E-03
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+ 19.50 6.919270E-05 -2.335794E-05 4.537762E-05
+ 19.55 4.615577E-05 -2.379820E-05 4.737785E-05
+ 19.60 2.274175E-05 -2.400813E-05 4.892828E-05
+ 19.65 -8.254765E-07 -2.398904E-05 5.002001E-05
+ 19.70 -2.432265E-05 -2.374455E-05 5.064632E-05
+ 19.75 -4.752972E-05 -2.328107E-05 5.080301E-05
+ 19.80 -7.023274E-05 -2.260785E-05 5.048970E-05
+ 19.85 -9.222658E-05 -2.173654E-05 4.971178E-05
+ 19.90 -1.133170E-04 -2.068037E-05 4.848106E-05
+ 19.95 -1.333220E-04 -1.945339E-05 4.681561E-05
+ 20.00 -1.520723E-04 -1.807004E-05 4.473819E-05
+ 20.05 -1.694124E-04 -1.654517E-05 4.227485E-05
+ 20.10 -1.852007E-04 -1.489453E-05 3.945292E-05
+ 20.15 -1.993112E-04 -1.313519E-05 3.630074E-05
+ 20.20 -2.116348E-04 -1.128577E-05 3.284805E-05
+ 20.25 -2.220816E-04 -9.366186E-06 2.912765E-05
+ 20.30 -2.305814E-04 -7.396904E-06 2.517590E-05
+ 20.35 -2.370841E-04 -5.398158E-06 2.103323E-05
+ 20.40 -2.415598E-04 -3.389282E-06 1.674293E-05
+ 20.45 -2.439976E-04 -1.388497E-06 1.234985E-05
+ 20.50 -2.444047E-04 5.868526E-07 7.898244E-06
+ 20.55 -2.428058E-04 2.519841E-06 3.430047E-06
+ 20.60 -2.392435E-04 4.393585E-06 -1.014279E-06
+ 20.65 -2.337781E-04 6.191231E-06 -5.395833E-06
+ 20.70 -2.264876E-04 7.896385E-06 -9.676003E-06
+ 20.75 -2.174670E-04 9.493808E-06 -1.381564E-05
+ 20.80 -2.068273E-04 1.097010E-05 -1.777496E-05
+ 20.85 -1.946928E-04 1.231404E-05 -2.151580E-05
+ 20.90 -1.811995E-04 1.351653E-05 -2.500212E-05
+ 20.95 -1.664932E-04 1.457009E-05 -2.820240E-05
+ 21.00 -1.507278E-04 1.546840E-05 -3.109015E-05
diff --git a/examples/USER/mgpt/in.bcc0 b/examples/USER/mgpt/in.bcc0
new file mode 100644
index 000000000..2e20888fd
--- /dev/null
+++ b/examples/USER/mgpt/in.bcc0
@@ -0,0 +1,68 @@
+# script for mgpt t=0 eos in bulk bcc structure
+
+echo screen
+
+units electron
+atom_style atomic
+
+# Atomic volume for MGPT potential in a.u.
+variable atomic_vol equal 121.6
+
+# Derive lattice constant from volume
+variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
+
+# Create bcc lattice with 5x5x5 unit cells (250 atoms)
+lattice bcc ${lattice_constant}
+region box block 0 5 0 5 0 5
+create_box 1 box
+create_atoms 1 box
+
+# Define potential for use in simulation
+pair_style mgpt
+
+# Set parameters for potential:
+# parameter files atomic volume
+#pair_coeff * * parmin potin ${atomic_vol}
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
+
+# Create velocities at 0 K
+velocity all create 0.0 87287
+
+# Set neighbor list parameters
+neighbor 0.1 bin
+neigh_modify every 1 delay 0 check yes
+
+# Set up microcanonical integrator
+fix 1 all nve
+
+# Dump coordinates to file every 50 timesteps
+dump id all atom 50 dump.bcc0
+
+# Output thermodynamical data every 10 timesteps
+thermo 10
+
+# Set output quantities and output format
+thermo_style custom step vol temp pe etotal press
+
+## Example: Output floating point number with 5 digits exponential notation.
+#thermo_modify format float %15.5e
+
+# Run 0 timesteps
+run 0
+
+# Convert energy to rydbergs and pressure to gpa
+
+variable natoms equal "count(all)"
+variable voltot equal "vol"
+variable atvol equal "v_voltot/v_natoms"
+variable etot equal "2.0*pe"
+variable etotry equal "v_etot/v_natoms"
+variable ptot equal "press"
+variable ptotgpa equal "v_ptot/1.0e+09"
+
+print "number of atoms = ${natoms}"
+print "atomic volume (a.u.) = ${atvol}"
+print "total energy (ry/atom) = ${etotry}"
+print "pressure (gpa) = ${ptotgpa}"
+print "${natoms} ${atvol} ${etot} ${ptotgpa}"
+print "${atvol} ${etotry} ${ptotgpa}"
diff --git a/examples/USER/mgpt/in.vac0-bcc b/examples/USER/mgpt/in.vac0-bcc
new file mode 100644
index 000000000..529506ab6
--- /dev/null
+++ b/examples/USER/mgpt/in.vac0-bcc
@@ -0,0 +1,76 @@
+# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
+# input for unrelaxed vacancy formation energy at constant atomic volume
+
+echo screen
+
+units electron
+atom_style atomic
+
+# Atomic volume for MGPT potential in a.u.
+variable atomic_vol equal 121.6
+
+# Derive effective lattice volume from atomic volume for 249-site cell
+variable lat_vol equal ${atomic_vol}*249/250
+
+# Derive lattice constant from lattice volume
+variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
+
+# Create bcc lattice with 5x5x5 unit cells (250 atoms)
+lattice bcc ${lattice_constant}
+region box block 0 5 0 5 0 5
+create_box 1 box
+create_atoms 1 box
+
+# Remove central atom from bcc lattice to create vacancy
+region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
+delete_atoms region vacancy
+
+# Define potential for use in simulation
+pair_style mgpt
+
+# Set parameters for potential:
+# parameter files atomic volume
+#pair_coeff * * parmin potin ${atomic_vol}
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
+
+# Create velocities at 0 K
+velocity all create 0.0 87287
+
+# Set neighbor list parameters
+neighbor 0.1 bin
+neigh_modify every 1 delay 0 check yes
+
+# Set up microcanonical integrator
+fix 1 all nve
+
+# Dump coordinates to file every 50 timesteps
+dump id all atom 50 dump.vac0-bcc
+
+# Output thermodynamical data every 10 timesteps
+thermo 10
+
+# Set output quantities and output format
+thermo_style custom step vol temp pe etotal press
+
+## Example: Output floating point number with 5 digits exponential notation.
+#thermo_modify format float %15.5e
+
+# Run 0 timesteps
+run 0
+
+# Convert energy to rydbergs and pressure to gpa
+
+variable natoms equal "count(all)"
+variable voltot equal "vol"
+variable atvol equal "v_voltot/v_natoms"
+variable etot equal "2.0*pe"
+variable etotry equal "v_etot/v_natoms"
+variable ptot equal "press"
+variable ptotgpa equal "v_ptot/1.0e+09"
+
+print "number of atoms = ${natoms}"
+print "atomic volume (a.u.) = ${atvol}"
+print "total energy (ry/atom) = ${etotry}"
+print "pressure (gpa) = ${ptotgpa}"
+print "${natoms} ${atvol} ${etot} ${ptotgpa}"
+print "${atvol} ${etotry} ${ptotgpa}"
diff --git a/examples/USER/mgpt/in.vacmin-bcc b/examples/USER/mgpt/in.vacmin-bcc
new file mode 100644
index 000000000..85fc72ff6
--- /dev/null
+++ b/examples/USER/mgpt/in.vacmin-bcc
@@ -0,0 +1,71 @@
+# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
+# input for relaxed vacancy formation energy at constant pressure
+
+echo screen
+
+units electron
+atom_style atomic
+
+# Atomic volume for MGPT potential
+variable atomic_vol equal 121.863
+
+# Derive effective lattice volume from atomic volume for 249-site cell
+variable lat_vol equal ${atomic_vol}*249/250
+
+# Derive lattice constant from lattice volume
+variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
+
+# Create bcc lattice with 5x5x5 unit cells (250 atoms)
+lattice bcc ${lattice_constant}
+region box block 0 5 0 5 0 5
+create_box 1 box
+create_atoms 1 box
+
+# Remove central atom from bcc lattice to create vacancy
+region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
+delete_atoms region vacancy
+
+# Define potential for use in simulation
+pair_style mgpt
+
+# Set parameters for potential:
+# parameter files atomic volume
+#pair_coeff * * parmin potin ${atomic_vol}
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
+
+# Set neighbor list parameters
+neighbor 0.1 bin
+neigh_modify every 1 delay 0 check yes
+
+# Dump coordinates to file every 50 timesteps
+dump id all atom 50 dump.vacmin-bcc
+
+# Output thermodynamical data every 10 timesteps
+thermo 10
+
+# Set output quantities and output format
+thermo_style custom step vol temp pe etotal press
+
+## Example: Output floating point number with 5 digits exponential notation.
+#thermo_modify format float %15.5e
+
+# minimize total energy
+min_style cg
+minimize 1.0e-10 1.0e-10 5000 10000
+
+# Convert energy to rydbergs and pressure to gpa
+
+variable natoms equal "count(all)"
+variable voltot equal "vol"
+variable atvol equal "v_voltot/v_natoms"
+variable etot equal "2.0*pe"
+variable etotry equal "v_etot/v_natoms"
+variable ptot equal "press"
+variable ptotgpa equal "v_ptot/1.0e+09"
+
+print "number of atoms = ${natoms}"
+print "atomic volume (a.u.) = ${atvol}"
+print "total energy (ry/atom) = ${etotry}"
+print "pressure (gpa) = ${ptotgpa}"
+print "${natoms} ${atvol} ${etot} ${ptotgpa}"
+print "${atvol} ${etotry} ${ptotgpa}"
diff --git a/examples/USER/mgpt/log.bcc0 b/examples/USER/mgpt/log.bcc0
new file mode 100644
index 000000000..4e4df5da4
--- /dev/null
+++ b/examples/USER/mgpt/log.bcc0
@@ -0,0 +1,53 @@
+LAMMPS (23 Oct 2015)
+# script for mgpt t=0 eos in bulk bcc structure
+
+echo screen
+Lattice spacing in x,y,z = 6.24196 6.24196 6.24196
+Created orthogonal box = (0 0 0) to (31.2098 31.2098 31.2098)
+ 1 by 1 by 1 MPI processor grid
+Created 250 atoms
+Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.1618
+ ghost atom cutoff = 13.1618
+ binsize = 6.58091 -> bins = 5 5 5
+Memory usage per processor = 3.54482 Mbytes
+Step Volume Temp PotEng TotEng Press
+ 0 30400 0 -74.412503 -74.412503 -1.1594626e+09
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 250 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1479 ave 1479 max 1479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 8000 ave 8000 max 8000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 16000 ave 16000 max 16000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 16000
+Ave neighs/atom = 64
+Neighbor list builds = 0
+Dangerous builds = 0
+number of atoms = 250
+atomic volume (a.u.) = 121.6
+total energy (ry/atom) = -0.59530002488734
+pressure (gpa) = -1.15946260887556
+250 121.6 -148.825006221835 -1.15946260887556
+121.6 -0.59530002488734 -1.15946260887556
+Total wall time: 0:00:00
diff --git a/examples/USER/mgpt/log.lammps b/examples/USER/mgpt/log.lammps
new file mode 100644
index 000000000..9485c36e4
--- /dev/null
+++ b/examples/USER/mgpt/log.lammps
@@ -0,0 +1,78 @@
+LAMMPS (23 Oct 2015)
+# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
+# input for relaxed vacancy formation energy at constant pressure
+
+echo screen
+Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
+Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
+ 1 by 1 by 1 MPI processor grid
+Created 250 atoms
+Deleted 1 atoms, new total = 249
+Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.1712
+ ghost atom cutoff = 13.1712
+ binsize = 6.58562 -> bins = 5 5 5
+Memory usage per processor = 4.66978 Mbytes
+Step Volume Temp PotEng TotEng Press
+ 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
+ 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
+ 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
+ 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
+ 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
+ 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
+ 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
+ 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
+ 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
+ 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
+ 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
+ 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
+ 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
+ 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
+ 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
+Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms
+
+92.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -73.9945109564 -74.0063705487 -74.0063705557
+ Force two-norm initial, final = 0.0366227 8.09081e-05
+ Force max component initial, final = 0.00730948 8.05242e-06
+ Final line search alpha, max atom move = 1 8.05242e-06
+ Iterations, force evaluations = 139 139
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43
+Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44
+Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04
+Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.00297 | | | 0.07
+
+Nlocal: 249 ave 249 max 249 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1479 ave 1479 max 1479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7936 ave 7936 max 7936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 15872 ave 15872 max 15872 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15872
+Ave neighs/atom = 63.743
+Neighbor list builds = 4
+Dangerous builds = 0
+number of atoms = 249
+atomic volume (a.u.) = 121.863
+total energy (ry/atom) = -0.594428679162064
+pressure (gpa) = -1.15783109519801
+249 121.863 -148.012741111354 -1.15783109519801
+121.863 -0.594428679162064 -1.15783109519801
+Total wall time: 0:00:04
diff --git a/examples/USER/mgpt/log.vac0-bcc b/examples/USER/mgpt/log.vac0-bcc
new file mode 100644
index 000000000..63880de45
--- /dev/null
+++ b/examples/USER/mgpt/log.vac0-bcc
@@ -0,0 +1,55 @@
+LAMMPS (23 Oct 2015)
+# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
+# input for unrelaxed vacancy formation energy at constant atomic volume
+
+echo screen
+Lattice spacing in x,y,z = 6.23363 6.23363 6.23363
+Created orthogonal box = (0 0 0) to (31.1681 31.1681 31.1681)
+ 1 by 1 by 1 MPI processor grid
+Created 250 atoms
+Deleted 1 atoms, new total = 249
+Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.1618
+ ghost atom cutoff = 13.1618
+ binsize = 6.58091 -> bins = 5 5 5
+Memory usage per processor = 3.54478 Mbytes
+Step Volume Temp PotEng TotEng Press
+ 0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 249 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 249 ave 249 max 249 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1479 ave 1479 max 1479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7936 ave 7936 max 7936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 15872 ave 15872 max 15872 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15872
+Ave neighs/atom = 63.743
+Neighbor list builds = 0
+Dangerous builds = 0
+number of atoms = 249
+atomic volume (a.u.) = 121.6
+total energy (ry/atom) = -0.594348488796036
+pressure (gpa) = -0.634267307139601
+249 121.6 -147.992773710213 -0.634267307139601
+121.6 -0.594348488796036 -0.634267307139601
+Total wall time: 0:00:00
diff --git a/examples/USER/mgpt/log.vacmin-bcc b/examples/USER/mgpt/log.vacmin-bcc
new file mode 100644
index 000000000..876b34eb1
--- /dev/null
+++ b/examples/USER/mgpt/log.vacmin-bcc
@@ -0,0 +1,78 @@
+LAMMPS (23 Oct 2015)
+# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
+# input for relaxed vacancy formation energy at constant pressure
+
+echo screen
+Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
+Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
+ 1 by 1 by 1 MPI processor grid
+Created 250 atoms
+Deleted 1 atoms, new total = 249
+Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.1712
+ ghost atom cutoff = 13.1712
+ binsize = 6.58562 -> bins = 5 5 5
+Memory usage per processor = 4.66978 Mbytes
+Step Volume Temp PotEng TotEng Press
+ 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
+ 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
+ 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
+ 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
+ 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
+ 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
+ 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
+ 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
+ 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
+ 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
+ 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
+ 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
+ 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
+ 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
+ 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
+Loop time of 4.22107 on 1 procs for 139 steps with 249 atoms
+
+92.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -73.9945109564 -74.0063705487 -74.0063705557
+ Force two-norm initial, final = 0.0366227 8.09081e-05
+ Force max component initial, final = 0.00730948 8.05242e-06
+ Final line search alpha, max atom move = 1 8.05242e-06
+ Iterations, force evaluations = 139 139
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.1973 | 4.1973 | 4.1973 | 0.0 | 99.44
+Neigh | 0.018799 | 0.018799 | 0.018799 | 0.0 | 0.45
+Comm | 0.0017059 | 0.0017059 | 0.0017059 | 0.0 | 0.04
+Output | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 0.02
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.002477 | | | 0.06
+
+Nlocal: 249 ave 249 max 249 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1479 ave 1479 max 1479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7936 ave 7936 max 7936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 15872 ave 15872 max 15872 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15872
+Ave neighs/atom = 63.743
+Neighbor list builds = 4
+Dangerous builds = 0
+number of atoms = 249
+atomic volume (a.u.) = 121.863
+total energy (ry/atom) = -0.594428679162064
+pressure (gpa) = -1.15783109519801
+249 121.863 -148.012741111354 -1.15783109519801
+121.863 -0.594428679162064 -1.15783109519801
+Total wall time: 0:00:04
diff --git a/examples/USER/smtbq/data.Alpha b/examples/USER/smtbq/data.Alpha
new file mode 100755
index 000000000..735f33c36
--- /dev/null
+++ b/examples/USER/smtbq/data.Alpha
@@ -0,0 +1,1811 @@
+
+ 1800 atoms
+ 2 atom types
+
+ 0.00 0.237690E+02 xlo xhi
+ 0.00 0.247015E+02 ylo yhi
+ 0.00 0.259564E+02 zlo zhi
+ 0.0 0.0 0.0 xy xz yz
+
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+1652 2 2.70 -1.9015200000 10.2922789113 -6.7321384253
+1653 1 -1.80 -3.3566106420 7.5476712016 -7.5706166667
+1654 1 -1.80 -5.7335106420 11.6645827661 -7.5706166667
+1655 1 -1.80 1.2029253210 4.6909050979 -7.5706166667
+1656 1 -1.80 -1.1739746790 8.8078166624 -7.5706166667
+1657 1 -1.80 -1.1739746790 6.2875257408 -7.5706166667
+1658 1 -1.80 -3.5508746790 10.4044373053 -7.5706166667
+1659 2 2.70 -1.9015200000 4.8030634919 -8.4090949080
+1660 2 2.70 -4.2784200000 8.9199750564 -8.4090949080
+1661 2 2.70 -1.9015200000 7.5476712016 -8.8951717587
+1662 2 2.70 -4.2784200000 11.6645827661 -8.8951717587
+1663 1 -1.80 -0.4464293580 4.8030634919 -9.7336500000
+1664 1 -1.80 -2.8233293580 8.9199750564 -9.7336500000
+1665 1 -1.80 -2.6290653210 6.0632089527 -9.7336500000
+1666 1 -1.80 -5.0059653210 10.1801205172 -9.7336500000
+1667 1 -1.80 -0.2521653210 7.6598295957 -9.7336500000
+1668 1 -1.80 -2.6290653210 11.7767411602 -9.7336500000
+1669 2 2.70 0.4753800000 6.1753673468 -10.5721282413
+1670 2 2.70 -1.9015200000 10.2922789113 -10.5721282413
+1671 2 2.70 -1.9015200000 4.8030634919 -11.0582050920
+1672 2 2.70 -4.2784200000 8.9199750564 -11.0582050920
+1673 1 -1.80 -3.5508746790 7.4355128075 -11.8966833333
+1674 1 -1.80 -5.9277746790 11.5524243721 -11.8966833333
+1675 1 -1.80 1.2029253210 4.9152218860 -11.8966833333
+1676 1 -1.80 -1.1739746790 9.0321334505 -11.8966833333
+1677 1 -1.80 -0.9797106420 6.1753673468 -11.8966833333
+1678 1 -1.80 -3.3566106420 10.2922789113 -11.8966833333
+1679 2 2.70 -1.9015200000 7.5476712016 -12.7351615747
+1680 2 2.70 -4.2784200000 11.6645827661 -12.7351615747
+1681 2 2.70 5.2291800000 6.1753673468 -0.2430384253
+1682 2 2.70 2.8522800000 10.2922789113 -0.2430384253
+1683 1 -1.80 4.3073706420 7.5476712016 -1.0815166667
+1684 1 -1.80 1.9304706420 11.6645827661 -1.0815166667
+1685 1 -1.80 4.5016346790 4.6909050979 -1.0815166667
+1686 1 -1.80 2.1247346790 8.8078166624 -1.0815166667
+1687 1 -1.80 2.1247346790 6.2875257408 -1.0815166667
+1688 1 -1.80 -0.2521653210 10.4044373053 -1.0815166667
+1689 2 2.70 2.8522800000 4.8030634919 -1.9199949080
+1690 2 2.70 0.4753800000 8.9199750564 -1.9199949080
+1691 2 2.70 2.8522800000 7.5476712016 -2.4060717587
+1692 2 2.70 0.4753800000 11.6645827661 -2.4060717587
+1693 1 -1.80 3.5798253210 6.0632089527 -3.2445500000
+1694 1 -1.80 1.2029253210 10.1801205172 -3.2445500000
+1695 1 -1.80 6.1509893580 4.8030634919 -3.2445500000
+1696 1 -1.80 3.7740893580 8.9199750564 -3.2445500000
+1697 1 -1.80 1.2029253210 7.6598295957 -3.2445500000
+1698 1 -1.80 -1.1739746790 11.7767411602 -3.2445500000
+1699 2 2.70 5.2291800000 6.1753673468 -4.0830282413
+1700 2 2.70 2.8522800000 10.2922789113 -4.0830282413
+1701 2 2.70 2.8522800000 4.8030634919 -4.5691050920
+1702 2 2.70 0.4753800000 8.9199750564 -4.5691050920
+1703 1 -1.80 4.5016346790 4.9152218860 -5.4075833333
+1704 1 -1.80 2.1247346790 9.0321334505 -5.4075833333
+1705 1 -1.80 4.5016346790 7.4355128075 -5.4075833333
+1706 1 -1.80 2.1247346790 11.5524243721 -5.4075833333
+1707 1 -1.80 1.9304706420 6.1753673468 -5.4075833333
+1708 1 -1.80 -0.4464293580 10.2922789113 -5.4075833333
+1709 2 2.70 2.8522800000 7.5476712016 -6.2460615747
+1710 2 2.70 0.4753800000 11.6645827661 -6.2460615747
+1711 2 2.70 5.2291800000 6.1753673468 -6.7321384253
+1712 2 2.70 2.8522800000 10.2922789113 -6.7321384253
+1713 1 -1.80 1.3971893580 7.5476712016 -7.5706166667
+1714 1 -1.80 -0.9797106420 11.6645827661 -7.5706166667
+1715 1 -1.80 5.9567253210 4.6909050979 -7.5706166667
+1716 1 -1.80 3.5798253210 8.8078166624 -7.5706166667
+1717 1 -1.80 3.5798253210 6.2875257408 -7.5706166667
+1718 1 -1.80 1.2029253210 10.4044373053 -7.5706166667
+1719 2 2.70 2.8522800000 4.8030634919 -8.4090949080
+1720 2 2.70 0.4753800000 8.9199750564 -8.4090949080
+1721 2 2.70 2.8522800000 7.5476712016 -8.8951717587
+1722 2 2.70 0.4753800000 11.6645827661 -8.8951717587
+1723 1 -1.80 4.3073706420 4.8030634919 -9.7336500000
+1724 1 -1.80 1.9304706420 8.9199750564 -9.7336500000
+1725 1 -1.80 2.1247346790 6.0632089527 -9.7336500000
+1726 1 -1.80 -0.2521653210 10.1801205172 -9.7336500000
+1727 1 -1.80 4.5016346790 7.6598295957 -9.7336500000
+1728 1 -1.80 2.1247346790 11.7767411602 -9.7336500000
+1729 2 2.70 5.2291800000 6.1753673468 -10.5721282413
+1730 2 2.70 2.8522800000 10.2922789113 -10.5721282413
+1731 2 2.70 2.8522800000 4.8030634919 -11.0582050920
+1732 2 2.70 0.4753800000 8.9199750564 -11.0582050920
+1733 1 -1.80 1.2029253210 7.4355128075 -11.8966833333
+1734 1 -1.80 -1.1739746790 11.5524243721 -11.8966833333
+1735 1 -1.80 5.9567253210 4.9152218860 -11.8966833333
+1736 1 -1.80 3.5798253210 9.0321334505 -11.8966833333
+1737 1 -1.80 3.7740893580 6.1753673468 -11.8966833333
+1738 1 -1.80 1.3971893580 10.2922789113 -11.8966833333
+1739 2 2.70 2.8522800000 7.5476712016 -12.7351615747
+1740 2 2.70 0.4753800000 11.6645827661 -12.7351615747
+1741 2 2.70 9.9829800000 6.1753673468 -0.2430384253
+1742 2 2.70 7.6060800000 10.2922789113 -0.2430384253
+1743 1 -1.80 9.0611706420 7.5476712016 -1.0815166667
+1744 1 -1.80 6.6842706420 11.6645827661 -1.0815166667
+1745 1 -1.80 9.2554346790 4.6909050979 -1.0815166667
+1746 1 -1.80 6.8785346790 8.8078166624 -1.0815166667
+1747 1 -1.80 6.8785346790 6.2875257408 -1.0815166667
+1748 1 -1.80 4.5016346790 10.4044373053 -1.0815166667
+1749 2 2.70 7.6060800000 4.8030634919 -1.9199949080
+1750 2 2.70 5.2291800000 8.9199750564 -1.9199949080
+1751 2 2.70 7.6060800000 7.5476712016 -2.4060717587
+1752 2 2.70 5.2291800000 11.6645827661 -2.4060717587
+1753 1 -1.80 8.3336253210 6.0632089527 -3.2445500000
+1754 1 -1.80 5.9567253210 10.1801205172 -3.2445500000
+1755 1 -1.80 10.9047893580 4.8030634919 -3.2445500000
+1756 1 -1.80 8.5278893580 8.9199750564 -3.2445500000
+1757 1 -1.80 5.9567253210 7.6598295957 -3.2445500000
+1758 1 -1.80 3.5798253210 11.7767411602 -3.2445500000
+1759 2 2.70 9.9829800000 6.1753673468 -4.0830282413
+1760 2 2.70 7.6060800000 10.2922789113 -4.0830282413
+1761 2 2.70 7.6060800000 4.8030634919 -4.5691050920
+1762 2 2.70 5.2291800000 8.9199750564 -4.5691050920
+1763 1 -1.80 9.2554346790 4.9152218860 -5.4075833333
+1764 1 -1.80 6.8785346790 9.0321334505 -5.4075833333
+1765 1 -1.80 9.2554346790 7.4355128075 -5.4075833333
+1766 1 -1.80 6.8785346790 11.5524243721 -5.4075833333
+1767 1 -1.80 6.6842706420 6.1753673468 -5.4075833333
+1768 1 -1.80 4.3073706420 10.2922789113 -5.4075833333
+1769 2 2.70 7.6060800000 7.5476712016 -6.2460615747
+1770 2 2.70 5.2291800000 11.6645827661 -6.2460615747
+1771 2 2.70 9.9829800000 6.1753673468 -6.7321384253
+1772 2 2.70 7.6060800000 10.2922789113 -6.7321384253
+1773 1 -1.80 6.1509893580 7.5476712016 -7.5706166667
+1774 1 -1.80 3.7740893580 11.6645827661 -7.5706166667
+1775 1 -1.80 10.7105253210 4.6909050979 -7.5706166667
+1776 1 -1.80 8.3336253210 8.8078166624 -7.5706166667
+1777 1 -1.80 8.3336253210 6.2875257408 -7.5706166667
+1778 1 -1.80 5.9567253210 10.4044373053 -7.5706166667
+1779 2 2.70 7.6060800000 4.8030634919 -8.4090949080
+1780 2 2.70 5.2291800000 8.9199750564 -8.4090949080
+1781 2 2.70 7.6060800000 7.5476712016 -8.8951717587
+1782 2 2.70 5.2291800000 11.6645827661 -8.8951717587
+1783 1 -1.80 9.0611706420 4.8030634919 -9.7336500000
+1784 1 -1.80 6.6842706420 8.9199750564 -9.7336500000
+1785 1 -1.80 6.8785346790 6.0632089527 -9.7336500000
+1786 1 -1.80 4.5016346790 10.1801205172 -9.7336500000
+1787 1 -1.80 9.2554346790 7.6598295957 -9.7336500000
+1788 1 -1.80 6.8785346790 11.7767411602 -9.7336500000
+1789 2 2.70 9.9829800000 6.1753673468 -10.5721282413
+1790 2 2.70 7.6060800000 10.2922789113 -10.5721282413
+1791 2 2.70 7.6060800000 4.8030634919 -11.0582050920
+1792 2 2.70 5.2291800000 8.9199750564 -11.0582050920
+1793 1 -1.80 5.9567253210 7.4355128075 -11.8966833333
+1794 1 -1.80 3.5798253210 11.5524243721 -11.8966833333
+1795 1 -1.80 10.7105253210 4.9152218860 -11.8966833333
+1796 1 -1.80 8.3336253210 9.0321334505 -11.8966833333
+1797 1 -1.80 8.5278893580 6.1753673468 -11.8966833333
+1798 1 -1.80 6.1509893580 10.2922789113 -11.8966833333
+1799 2 2.70 7.6060800000 7.5476712016 -12.7351615747
+1800 2 2.70 5.2291800000 11.6645827661 -12.7351615747
diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/USER/smtbq/ffield.smtbq.Al
new file mode 100755
index 000000000..f63b6c43b
--- /dev/null
+++ b/examples/USER/smtbq/ffield.smtbq.Al
@@ -0,0 +1,34 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# SMTBQ parameter for Al-Al interaction.
+# Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ.
+# year: 2014
+# =========================================================================
+' Nombre.de.type.d.atome..........:' 1
+' ====== atomic parameters ======= '
+' Cation.de.l.oxyde..Stoechio.....:' 'Al' 1
+' Qform.....masse.................:' 3.0 26.98
+' Param.QEq.(ne,.Chi,.J,.R_eff)...:' 3 1.19258 11.05345 0.57701
+' Nbre.d.etats.partage.par.cation.:' 3
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Al' 'Al' 'second_moment' 'metal'
+' Potentiel.Cat-Ox.(A,.p,.Ksi,.q).:' 0.1221 8.612 1.316 2.516
+' Pot..Cat-Ox.(rc1,.rc2,.r0).Iota.:' 5.6 7.0 2.863 2.0
+' ======== Parametre tab ========= '
+' Rcoul...........................:' 11.1714
+' rmin...dr.......................:' 1.18845 0.001
+' ======== IFQM Parameter ======== '
+' Frenquency.Q.resolution..........' 0
+' loopmax.-.precision..............' 5000 0.0002
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.5 3.2
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' 0.0
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAllParallel'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== END's parameters =========================
+
diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/USER/smtbq/ffield.smtbq.Al2O3
new file mode 100755
index 000000000..9c26ade9e
--- /dev/null
+++ b/examples/USER/smtbq/ffield.smtbq.Al2O3
@@ -0,0 +1,56 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# SMTBQ parameter for AlO interaction with a limit length 'rc2sm=dc2**2'.
+# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ.
+#
+# Presentation atom : nature
+# q, qmin, qmax, masse
+# parameter QEq : Chi, J, R_eff
+# Parameter SM : A, p, Ksi, q
+# CutOff SM : dc1, dc2, r0
+# =========================================================================
+# -------------------------- Begin's parameters ---------------------------
+' Number.of.atoms.type............:' 2
+' ====== atomic parameters ======= '
+' 1st.element.(Oxygen).Stoechio...:' 'O' 3
+' Qform.....mass..................:' -2.0 16.00
+' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
+' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 4. 3.00 0.529 0.529 0.529
+' Number.of.shared.state.by.ions..:' 3
+' -------------------------------- '
+' 2nd.element.(metal).Stoechio....:' 'Al' 2
+' Qform.....mass..................:' 3.0 26.98
+' Param.QEq.(ne,.Chi0,.Ji0,.R_eff):' 3 1.19009 11.1903 0.56619
+' Number.of.shared.state.by.ions..:' 4
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Al' 'O' 'second_moment' 'oxide'
+' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.18176 8.80041 0.26044 1.58851
+' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 4. 5.6 1.91
+' -------------------------------- '
+' atom1..atom2..potential..........' 'O' 'O' 'buck'
+' Potentiel.O-O...(C,.Rho)........:' 580.440 0.3540
+' ======== Parametre tab ========= '
+' Rcoul=a*rc(SMASH)...............:' 11.1714
+' rmin...dr.......................:' 1.18845 0.001
+' ======== IFQM Parameter ======== '
+' Nevery.charge.calculation........' 1
+' loopmax....precision.............' 7000 0.000001
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.5 3.2
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' -1.8
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAll'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== FIN des parametres =========================
+
+#Possible QInit modes
+# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
+#any other name would lead to either 0 charges or charge read from the lammps atomic position file
+#Possible QEq modes | parameters
+# QEqAll | no parameters
+# QEqAllParallel | no parameters
+# Surface | zlim (QEq only for z>zlim)
diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/USER/smtbq/ffield.smtbq.TiO2
new file mode 100755
index 000000000..4c8d9df53
--- /dev/null
+++ b/examples/USER/smtbq/ffield.smtbq.TiO2
@@ -0,0 +1,53 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# ========================================================================
+# SMTBQ parameter for Ti-O interaction with a limit length 'rc2sm=dc2**2'.
+# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ
+# september 2014
+# ========================================================================
+' Number.of.atoms.type............:' 2
+' ====== atomic parameters ======= '
+' 1st.element.(Oxygen).Stoechio...:' 'O' 2
+' Qform.....mass..................:' -2.0 16.00
+' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
+' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 3. 2.00 0.52 0.54348 0.58
+' Number.of.shared.state.by.ions..:' 3
+' -------------------------------- '
+' 2nd.element.(metal).Stoechio....:' 'Ti' 1
+' Qform.....mass..................:' 4.0 26.98
+' Param.QEq.(nq,.Chi0,.Ji0,.R_eff):' 3 0.00 10.572 0.734
+' Number.of.shared.state.by.ions..:' 5
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Ti' 'O' 'second_moment' 'oxide'
+' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.134 12.609 0.5434 2.0965
+' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 3.6 6.0 1.95
+' -------------------------------- '
+' atom1..atom2..potential..........' 'O' 'O' 'buckPlusAttr'
+' Potential.O-O...(C,.Rho)........:' 580.440 0.3540
+' Potential.O-O...(D.B.r1OO.r2OO).:' -20.86 -0.916 1.4 1.8
+' ======== Tab Parameter ========= '
+' Rcoul=a*rc(SMASH)...............:' 12.1744
+' rmin...dr.......................:' 1.0675 0.001
+' ======== IFQM Parameter ======== '
+' Nevery.charge.calculation........' 1
+' loopmax....precision.............' 7000 0.000001
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.0 3.5
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' -1.0
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAll'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== END's parameters =========================
+
+#Possible QInit modes
+# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
+#any other name would lead to either 0 charges or charge read from the lammps atomic position file
+#Possible QEq modes | parameters
+# QEqAll | no parameters
+# QEqAllParallel | no parameters
+# Surface | zlim (QEq only for z>zlim)
+# BulkFromSlab | zlim1 zlim2 (QEq only for zlim1<z<zlim2)
diff --git a/examples/USER/smtbq/in.smtbq.Al b/examples/USER/smtbq/in.smtbq.Al
new file mode 100755
index 000000000..c24224091
--- /dev/null
+++ b/examples/USER/smtbq/in.smtbq.Al
@@ -0,0 +1,77 @@
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+variable dt equal 0.0002
+
+#Constante
+variable rac3 equal sqrt(3.0)
+variable rac1_2 equal sqrt(0.5)
+variable rac3_2 equal sqrt(1.5)
+
+#Structure
+variable a equal 4.05
+
+variable nx equal 10
+variable ny equal 7
+variable nz equal 4
+
+variable bx equal ${a}*${nx}*${rac1_2}
+variable by equal ${a}*${ny}*${rac3_2}
+variable bz equal ${a}*${nz}*${rac3}
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+
+lattice sc 1.0
+region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+create_box 1 box_vide
+
+# Aluminium atoms z = [111]
+lattice custom ${a} a1 ${rac1_2} 0.0 0.0 &
+ a2 0.0 ${rac3_2} 0.0 &
+ a3 0.0 0.0 ${rac3} &
+ basis 0.0 0.0 0.0 &
+ basis 0.5 0.5 0.0 &
+ basis 0.5 0.166666667 0.33333 &
+ basis 0.0 0.666666667 0.33333 &
+ basis 0.0 0.333333333 0.66667 &
+ basis 0.5 0.833333333 0.66667
+
+create_atoms 1 region box_vide
+
+mass 1 26.98
+
+velocity all create ${T_depart} 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al Al
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+
+thermo_style custom step temp press pe ke etotal lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+
+#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+
+unfix 3
+#thermo 15
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-8 1.0e-10 1000 10000
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+
diff --git a/examples/USER/smtbq/in.smtbq.Al2O3 b/examples/USER/smtbq/in.smtbq.Al2O3
new file mode 100755
index 000000000..76ab3c86d
--- /dev/null
+++ b/examples/USER/smtbq/in.smtbq.Al2O3
@@ -0,0 +1,55 @@
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.Alpha
+# ^ Orthorombic box of corundum strcture
+
+mass 1 16.00
+group Oxy type 1
+compute chargeOxy Oxy property/atom q
+compute q_Oxy Oxy reduce ave c_chargeOxy
+
+mass 2 26.98
+group Al type 2
+compute chargeAl Al property/atom q
+compute q_Al Al reduce ave c_chargeAl
+
+velocity all create ${T_depart} 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+
+thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+
+unfix 3
+thermo 1
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-3 1.0e-5 1000 10000
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+
diff --git a/examples/USER/smtbq/in.smtbq.TiO2 b/examples/USER/smtbq/in.smtbq.TiO2
new file mode 100755
index 000000000..a3261216a
--- /dev/null
+++ b/examples/USER/smtbq/in.smtbq.TiO2
@@ -0,0 +1,97 @@
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+variable a equal 4.5937
+variable c equal 2.9587
+variable ca equal ${c}/${a}
+
+variable nx equal 6
+variable ny equal 6
+variable nz equal 11
+
+variable bx equal ${a}*${nx}
+variable by equal ${a}*${ny}
+variable bz equal ${c}*${nz}
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+
+lattice sc 1.0
+region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+create_box 2 box_vide
+
+#lattice sc 1.0
+#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
+
+# titanium atoms
+lattice custom ${a} origin 0.0 0.0 0.0 &
+ orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
+ a1 1.0 0.0 0.0 &
+ a2 0.0 1.0 0.0 &
+ a3 0.0 0.0 ${ca} &
+ basis 0.0 0.0 0.0 &
+ basis 0.5 0.5 0.5
+
+create_atoms 2 region box_vide
+
+# Oxygen atoms
+lattice custom ${a} origin 0.0 0.0 0.0 &
+ orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
+ a1 1.0 0.0 0.0 &
+ a2 0.0 1.0 0.0 &
+ a3 0.0 0.0 ${ca} &
+ basis 0.30478 0.30478 0.0 &
+ basis 0.69522 0.69522 0.0 &
+ basis 0.19522 0.80478 0.5 &
+ basis 0.80478 0.19522 0.5
+
+create_atoms 1 region box_vide
+
+
+mass 1 16.00
+group Oxy type 1
+compute chargeOxy Oxy property/atom q
+compute q_Oxy Oxy reduce ave c_chargeOxy
+
+mass 2 47.867
+group Ti type 2
+compute chargeTi Ti property/atom q
+compute q_Ti Ti reduce ave c_chargeTi
+
+velocity all create ${T_depart} 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.TiO2 O Ti
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+
+thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+
+#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+
+unfix 3
+#thermo 15
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-3 1.0e-5 1000 10000
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+
diff --git a/examples/USER/smtbq/log.smtbq.Al b/examples/USER/smtbq/log.smtbq.Al
new file mode 100644
index 000000000..b52a37c2e
--- /dev/null
+++ b/examples/USER/smtbq/log.smtbq.Al
@@ -0,0 +1,279 @@
+LAMMPS (23 Oct 2015)
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+variable dt equal 0.0002
+
+#Constante
+variable rac3 equal sqrt(3.0)
+variable rac1_2 equal sqrt(0.5)
+variable rac3_2 equal sqrt(1.5)
+
+#Structure
+variable a equal 4.05
+
+variable nx equal 10
+variable ny equal 7
+variable nz equal 4
+
+variable bx equal ${a}*${nx}*${rac1_2}
+variable bx equal 4.05*${nx}*${rac1_2}
+variable bx equal 4.05*10*${rac1_2}
+variable bx equal 4.05*10*0.707106781186548
+variable by equal ${a}*${ny}*${rac3_2}
+variable by equal 4.05*${ny}*${rac3_2}
+variable by equal 4.05*7*${rac3_2}
+variable by equal 4.05*7*1.22474487139159
+variable bz equal ${a}*${nz}*${rac3}
+variable bz equal 4.05*${nz}*${rac3}
+variable bz equal 4.05*4*${rac3}
+variable bz equal 4.05*4*1.73205080756888
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+
+lattice sc 1.0
+Lattice spacing in x,y,z = 1 1 1
+region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 28.6378246380552 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 28.0592230826159 0.0 0.0 0.0
+create_box 1 box_vide
+Created triclinic box = (0 0 0) to (28.6378 34.7215 28.0592) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+
+# Aluminium atoms z = [111]
+lattice custom ${a} a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
+lattice custom 4.05 a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
+lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
+lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
+lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 1.73205080756888 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
+Lattice spacing in x,y,z = 2.86378 4.96022 7.01481
+
+create_atoms 1 region box_vide
+Created 1680 atoms
+
+mass 1 26.98
+
+velocity all create ${T_depart} 277387
+velocity all create 300 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al Al
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+timestep 0.0002
+
+thermo_style custom step temp press pe ke etotal lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+
+#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 6 5
+Memory usage per processor = 4.52298 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
+ 0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 1 299.98323 729.90439 -5600.8505 65.104695 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 2 299.93288 731.82072 -5600.8395 65.093767 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 3 299.84896 735.01448 -5600.8213 65.075556 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 4 299.7315 739.48472 -5600.7958 65.050064 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 5 299.58053 745.23012 -5600.7631 65.017299 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 6 299.39609 752.24896 -5600.723 64.977269 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 7 299.17822 760.5391 -5600.6757 64.929985 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 8 298.92698 770.098 -5600.6212 64.875459 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 9 298.64244 780.92261 -5600.5595 64.813707 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
+Loop time of 5.10336 on 1 procs for 10 steps with 1680 atoms
+
+Performance: 0.034 ns/day, 708.800 hours/ns, 1.959 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.1023 | 5.1023 | 5.1023 | 0.0 | 99.98
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
+Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
+Modify | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.01
+Other | | 0.0001056 | | | 0.00
+
+Nlocal: 1680 ave 1680 max 1680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7518 ave 7518 max 7518 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 638400 ave 638400 max 638400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 638400
+Ave neighs/atom = 380
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 3
+#thermo 15
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-8 1.0e-10 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 6 5
+Memory usage per processor = 5.64798 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
+ 10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
+ 11 298.32468 2483.3228 -5600.5212 64.744743 -5535.7764 28.617938 34.697425 28.039771 27842.617
+ 12 298.32468 3102.6624 -5600.6242 64.744743 -5535.8795 28.594201 34.68783 28.048729 27820.715
+ 13 298.32468 1681.0688 -5600.6477 64.744743 -5535.903 28.619779 34.708131 28.055945 27869.065
+ 14 298.32468 949.90841 -5600.6635 64.744743 -5535.9187 28.648416 34.718691 28.044409 27893.966
+ 15 298.32468 2009.1662 -5600.7072 64.744743 -5535.9625 28.652241 34.703261 28.01635 27857.391
+ 16 298.32468 2867.1434 -5600.7192 64.744743 -5535.9744 28.626861 34.69005 28.022309 27828.038
+ 17 298.32468 2480.3207 -5600.7238 64.744743 -5535.9791 28.618046 34.695106 28.040113 27841.2
+ 18 298.32468 2482.4906 -5600.7249 64.744743 -5535.9802 28.614169 34.704237 28.036452 27841.119
+ 19 298.32468 2495.6209 -5600.7261 64.744743 -5535.9813 28.616207 34.697481 28.039453 27840.662
+ 20 298.32468 2210.2897 -5600.7271 64.744743 -5535.9823 28.620852 34.699678 28.042926 27850.393
+ 21 298.32468 2464.137 -5600.734 64.744743 -5535.9893 28.625239 34.687085 28.040022 27841.67
+ 22 298.32468 3091.7034 -5600.7471 64.744743 -5536.0024 28.623565 34.674943 28.02983 27820.181
+ 23 298.32468 2334.9443 -5600.7598 64.744743 -5536.0151 28.634413 34.684598 28.037298 27845.891
+ 24 298.32468 2462.2836 -5600.7767 64.744743 -5536.032 28.615834 34.692433 28.044664 27841.422
+ 25 298.32468 2652.08 -5600.7914 64.744743 -5536.0466 28.61528 34.695645 28.035991 27834.85
+ 26 298.32468 2365.4126 -5600.7923 64.744743 -5536.0476 28.618526 34.699347 28.039662 27844.623
+ 27 298.32468 2334.9429 -5600.7934 64.744743 -5536.0486 28.61826 34.698136 28.041941 27845.656
+ 28 298.32468 2501.1598 -5600.7937 64.744743 -5536.0489 28.616356 34.695993 28.039825 27839.982
+ 29 298.32468 2506.0962 -5600.794 64.744743 -5536.0493 28.617255 34.699031 28.036317 27839.811
+ 30 298.32468 2400.7588 -5600.7942 64.744743 -5536.0495 28.618372 34.698464 28.039299 27843.404
+ 31 298.32468 2499.8528 -5600.7945 64.744743 -5536.0497 28.61702 34.69385 28.040945 27840.021
+ 32 298.32468 2629.5393 -5600.7967 64.744743 -5536.0519 28.619399 34.691546 28.036003 27835.58
+ 33 298.32468 2397.5939 -5600.7973 64.744743 -5536.0526 28.621863 34.69535 28.03848 27843.488
+ 34 298.32468 2222.7714 -5600.8007 64.744743 -5536.056 28.609815 34.705091 28.048395 27849.426
+ 35 298.32468 2748.5871 -5600.8042 64.744743 -5536.0594 28.600322 34.6998 28.043876 27831.457
+ 36 298.32468 2661.1018 -5600.8166 64.744743 -5536.0719 28.615123 34.696499 28.034947 27834.344
+ 37 298.32468 2255.4994 -5600.8185 64.744743 -5536.0737 28.618919 34.702261 28.040497 27848.173
+ 38 298.32468 2260.815 -5600.8239 64.744743 -5536.0791 28.614993 34.70246 28.043972 27847.962
+ 39 298.32468 2549.2876 -5600.8248 64.744743 -5536.0801 28.612892 34.697988 28.039725 27838.113
+ 40 298.32468 2488.3825 -5600.8266 64.744743 -5536.0819 28.623347 34.695524 28.033557 27840.182
+ 41 298.32468 2400.9714 -5600.8283 64.744743 -5536.0835 28.619176 34.695733 28.040468 27843.155
+ 42 298.32468 2496.6566 -5600.8284 64.744743 -5536.0837 28.617629 34.694692 28.039536 27839.89
+ 43 298.32468 2486.2773 -5600.8285 64.744743 -5536.0838 28.617585 34.697413 28.037736 27840.243
+ 44 298.32468 2446.3916 -5600.8287 64.744743 -5536.0839 28.617115 34.696389 28.040393 27841.603
+ 45 298.32468 2547.2311 -5600.8288 64.744743 -5536.0841 28.615267 34.694882 28.039956 27838.161
+ 46 298.32468 2479.9982 -5600.8321 64.744743 -5536.0874 28.603008 34.71581 28.037344 27840.427
+ 47 298.32468 2449.645 -5600.8444 64.744743 -5536.0997 28.612743 34.683541 28.054837 27841.375
+ 48 298.32468 2682.7109 -5600.8695 64.744743 -5536.1248 28.617414 34.683477 28.042139 27833.265
+ 49 298.32468 2350.1707 -5600.8711 64.744743 -5536.1263 28.619236 34.694213 28.043092 27844.6
+ 50 298.32468 2486.1481 -5600.8719 64.744743 -5536.1271 28.615167 34.699435 28.038181 27839.955
+ 51 298.32468 2498.3384 -5600.8721 64.744743 -5536.1274 28.616069 34.696071 28.039596 27839.537
+ 52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
+Loop time of 36.9389 on 1 procs for 42 steps with 1680 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -5600.49050006 -5600.87213771 -5600.87218615
+ Force two-norm initial, final = 50.879 1.39888
+ Force max component initial, final = 29.3783 0.749036
+ Final line search alpha, max atom move = 0.0013373 0.00100168
+ Iterations, force evaluations = 42 71
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 36.918 | 36.918 | 36.918 | 0.0 | 99.94
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0033035 | 0.0033035 | 0.0033035 | 0.0 | 0.01
+Output | 0.0011785 | 0.0011785 | 0.0011785 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.01603 | | | 0.04
+
+Nlocal: 1680 ave 1680 max 1680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7518 ave 7518 max 7518 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 638400 ave 638400 max 638400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 638400
+Ave neighs/atom = 380
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 6 5
+Memory usage per processor = 4.52298 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
+ 52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 53 298.28341 2444.4342 -5600.8632 64.735788 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 54 298.20852 2447.019 -5600.847 64.719534 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 55 298.1 2450.8786 -5600.8234 64.695982 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 56 297.95788 2456.0119 -5600.7926 64.665139 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 57 297.7822 2462.4173 -5600.7545 64.62701 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 58 297.57298 2470.0928 -5600.709 64.581604 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 59 297.33028 2479.0363 -5600.6564 64.528932 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 60 297.05416 2489.245 -5600.5964 64.469006 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 61 296.74469 2500.7159 -5600.5293 64.401842 -5536.1274 28.617616 34.696737 28.039439 27841.421
+ 62 296.40194 2513.4457 -5600.4549 64.327455 -5536.1274 28.617616 34.696737 28.039439 27841.421
+Loop time of 5.13028 on 1 procs for 10 steps with 1680 atoms
+
+Performance: 0.034 ns/day, 712.539 hours/ns, 1.949 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.1292 | 5.1292 | 5.1292 | 0.0 | 99.98
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.01
+Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
+Modify | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
+Other | | 0.0001016 | | | 0.00
+
+Nlocal: 1680 ave 1680 max 1680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7518 ave 7518 max 7518 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 638400 ave 638400 max 638400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 638400
+Ave neighs/atom = 380
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:49
diff --git a/examples/USER/smtbq/log.smtbq.Al2O3 b/examples/USER/smtbq/log.smtbq.Al2O3
new file mode 100644
index 000000000..b7d2ad5ae
--- /dev/null
+++ b/examples/USER/smtbq/log.smtbq.Al2O3
@@ -0,0 +1,210 @@
+LAMMPS (23 Oct 2015)
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.Alpha
+ triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1800 atoms
+# ^ Orthorombic box of corundum strcture
+
+mass 1 16.00
+group Oxy type 1
+1080 atoms in group Oxy
+compute chargeOxy Oxy property/atom q
+compute q_Oxy Oxy reduce ave c_chargeOxy
+
+mass 2 26.98
+group Al type 2
+720 atoms in group Al
+compute chargeAl Al property/atom q
+compute q_Al Al reduce ave c_chargeAl
+
+velocity all create ${T_depart} 277387
+velocity all create 300 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+timestep 0.0002
+
+thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+
+#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 5 5
+Memory usage per processor = 4.12573 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
+ 0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78
+ 1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78
+ 2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78
+ 3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78
+ 4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78
+ 5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78
+ 6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78
+ 7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78
+ 8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78
+ 9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78
+ 10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
+Loop time of 169.694 on 1 procs for 10 steps with 1800 atoms
+
+Performance: 0.001 ns/day, 23568.600 hours/ns, 0.059 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 169.69 | 169.69 | 169.69 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00075507 | 0.00075507 | 0.00075507 | 0.0 | 0.00
+Output | 0.00078607 | 0.00078607 | 0.00078607 | 0.0 | 0.00
+Modify | 0.00034666 | 0.00034666 | 0.00034666 | 0.0 | 0.00
+Other | | 0.0001752 | | | 0.00
+
+Nlocal: 1800 ave 1800 max 1800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11490 ave 11490 max 11490 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.4472e+06 ave 1.4472e+06 max 1.4472e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1447200
+Ave neighs/atom = 804
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 3
+thermo 1
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-3 1.0e-5 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 5 5
+Memory usage per processor = 5.50073 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
+ 10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
+ 11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
+Loop time of 25.4145 on 1 procs for 1 steps with 1800 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -11492.6369832 -11492.6369832 -11494.7221261
+ Force two-norm initial, final = 1453.27 1325.26
+ Force max component initial, final = 968.201 892.249
+ Final line search alpha, max atom move = 1.03284e-06 0.000921553
+ Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 25.414 | 25.414 | 25.414 | -nan |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00013995 | 0.00013995 | 0.00013995 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0005064 | | | 0.00
+
+Nlocal: 1800 ave 1800 max 1800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11408 ave 11408 max 11408 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.44456e+06 ave 1.44456e+06 max 1.44456e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1444562
+Ave neighs/atom = 802.534
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.6714
+ ghost atom cutoff = 11.6714
+ binsize = 5.8357 -> bins = 5 5 5
+Memory usage per processor = 4.37573 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
+ 11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
+ 12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17
+ 13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17
+ 14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17
+ 15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17
+ 16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17
+ 17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17
+ 18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17
+ 19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17
+ 20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17
+ 21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17
+Loop time of 170.699 on 1 procs for 10 steps with 1800 atoms
+
+Performance: 0.001 ns/day, 23708.143 hours/ns, 0.059 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 170.7 | 170.7 | 170.7 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00068879 | 0.00068879 | 0.00068879 | 0.0 | 0.00
+Output | 0.0008359 | 0.0008359 | 0.0008359 | 0.0 | 0.00
+Modify | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.00
+Other | | 0.0001593 | | | 0.00
+
+Nlocal: 1800 ave 1800 max 1800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11222 ave 11222 max 11222 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.44126e+06 ave 1.44126e+06 max 1.44126e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1441262
+Ave neighs/atom = 800.701
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:06:42
diff --git a/examples/USER/smtbq/log.smtbq.TiO2 b/examples/USER/smtbq/log.smtbq.TiO2
new file mode 100644
index 000000000..433a7ceab
--- /dev/null
+++ b/examples/USER/smtbq/log.smtbq.TiO2
@@ -0,0 +1,255 @@
+LAMMPS (23 Oct 2015)
+# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+variable a equal 4.5937
+variable c equal 2.9587
+variable ca equal ${c}/${a}
+variable ca equal 2.9587/${a}
+variable ca equal 2.9587/4.5937
+
+variable nx equal 6
+variable ny equal 6
+variable nz equal 11
+
+variable bx equal ${a}*${nx}
+variable bx equal 4.5937*${nx}
+variable bx equal 4.5937*6
+variable by equal ${a}*${ny}
+variable by equal 4.5937*${ny}
+variable by equal 4.5937*6
+variable bz equal ${c}*${nz}
+variable bz equal 2.9587*${nz}
+variable bz equal 2.9587*11
+# =======================================================================
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+
+lattice sc 1.0
+Lattice spacing in x,y,z = 1 1 1
+region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
+region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
+create_box 2 box_vide
+Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+
+#lattice sc 1.0
+#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
+
+# titanium atoms
+lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms 2 region box_vide
+Created 792 atoms
+
+# Oxygen atoms
+lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
+lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
+lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms 1 region box_vide
+Created 1584 atoms
+
+
+mass 1 16.00
+group Oxy type 1
+1584 atoms in group Oxy
+compute chargeOxy Oxy property/atom q
+compute q_Oxy Oxy reduce ave c_chargeOxy
+
+mass 2 47.867
+group Ti type 2
+792 atoms in group Ti
+compute chargeTi Ti property/atom q
+compute q_Ti Ti reduce ave c_chargeTi
+
+velocity all create ${T_depart} 277387
+velocity all create 300 277387
+
+pair_style smtbq
+pair_coeff * * ffield.smtbq.TiO2 O Ti
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check yes
+
+timestep ${dt}
+timestep 0.0002
+
+thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
+thermo_modify flush yes
+thermo 1
+
+
+#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.6744
+ ghost atom cutoff = 12.6744
+ binsize = 6.3372 -> bins = 5 5 6
+Memory usage per processor = 4.77264 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
+ 0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
+ 1 299.90455 44375.373 -15815.21 92.06855 -15723.142 2.552178 -1.276089 27.5622 27.5622 32.5457 24724.15
+ 2 299.63739 44392.241 -15815.128 91.986534 -15723.142 2.5521725 -1.2760863 27.5622 27.5622 32.5457 24724.15
+ 3 299.19899 44415.606 -15814.994 91.85195 -15723.142 2.5521616 -1.2760808 27.5622 27.5622 32.5457 24724.15
+ 4 298.59012 44445.345 -15814.808 91.665031 -15723.143 2.5521454 -1.2760727 27.5622 27.5622 32.5457 24724.15
+ 5 297.81185 44481.382 -15814.57 91.426105 -15723.144 2.5521238 -1.2760619 27.5622 27.5622 32.5457 24724.15
+ 6 296.86552 44523.683 -15814.28 91.135592 -15723.144 2.5520969 -1.2760484 27.5622 27.5622 32.5457 24724.15
+ 7 295.75281 44572.175 -15813.939 90.793996 -15723.145 2.5520648 -1.2760324 27.5622 27.5622 32.5457 24724.15
+ 8 294.47564 44626.778 -15813.548 90.401913 -15723.147 2.5520274 -1.2760137 27.5622 27.5622 32.5457 24724.15
+ 9 293.03623 44687.401 -15813.108 89.960027 -15723.148 2.5519849 -1.2759925 27.5622 27.5622 32.5457 24724.15
+ 10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
+Loop time of 570.52 on 1 procs for 10 steps with 2376 atoms
+
+Performance: 0.000 ns/day, 79238.948 hours/ns, 0.018 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 570.52 | 570.52 | 570.52 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00087428 | 0.00087428 | 0.00087428 | 0.0 | 0.00
+Output | 0.00091386 | 0.00091386 | 0.00091386 | 0.0 | 0.00
+Modify | 0.00045085 | 0.00045085 | 0.00045085 | 0.0 | 0.00
+Other | | 0.0001979 | | | 0.00
+
+Nlocal: 2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 13138 ave 13138 max 13138 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.9705e+06 ave 1.9705e+06 max 1.9705e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1970496
+Ave neighs/atom = 829.333
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 3
+#thermo 15
+fix 1 all box/relax tri 0.0 vmax 0.001
+minimize 1.0e-3 1.0e-5 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.6744
+ ghost atom cutoff = 12.6744
+ binsize = 6.3372 -> bins = 5 5 6
+Memory usage per processor = 6.14764 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
+ 10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
+ 11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
+Loop time of 80.5411 on 1 procs for 1 steps with 2376 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -15812.6183471 -15812.6183471 -15814.1085593
+ Force two-norm initial, final = 1104.2 951.386
+ Force max component initial, final = 759.352 657.815
+ Final line search alpha, max atom move = 1.31691e-06 0.000866285
+ Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 80.54 | 80.54 | 80.54 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00016761 | 0.00016761 | 0.00016761 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0006053 | | | 0.00
+
+Nlocal: 2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 13138 ave 13138 max 13138 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.96864e+06 ave 1.96864e+06 max 1.96864e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1968636
+Ave neighs/atom = 828.551
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 1
+thermo 1
+fix 3 all nve
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.6744
+ ghost atom cutoff = 12.6744
+ binsize = 6.3372 -> bins = 5 5 6
+Memory usage per processor = 5.02264 Mbytes
+Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
+ 11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
+ 12 289.69465 39072.309 -15813.575 88.934185 -15724.641 2.551372 -1.275686 27.582771 27.582775 32.578246 24785.834
+ 13 287.79928 39149.855 -15812.994 88.352321 -15724.642 2.5513146 -1.2756573 27.582771 27.582775 32.578246 24785.834
+ 14 285.75427 39232.968 -15812.368 87.724515 -15724.644 2.5512525 -1.2756262 27.582771 27.582775 32.578246 24785.834
+ 15 283.56312 39321.472 -15811.697 87.05185 -15724.645 2.5511856 -1.2755928 27.582771 27.582775 32.578246 24785.834
+ 16 281.22962 39415.185 -15810.983 86.335481 -15724.647 2.5511143 -1.2755571 27.582771 27.582775 32.578246 24785.834
+ 17 278.75777 39513.921 -15810.226 85.57664 -15724.649 2.5510384 -1.2755192 27.582771 27.582775 32.578246 24785.834
+ 18 276.15182 39617.471 -15809.428 84.776632 -15724.651 2.5509583 -1.2754791 27.582771 27.582775 32.578246 24785.834
+ 19 273.41625 39725.622 -15808.591 83.936831 -15724.654 2.5508739 -1.275437 27.582771 27.582775 32.578246 24785.834
+ 20 270.55575 39838.144 -15807.715 83.058679 -15724.656 2.5507855 -1.2753928 27.582771 27.582775 32.578246 24785.834
+ 21 267.57523 39954.804 -15806.802 82.14368 -15724.659 2.5506932 -1.2753466 27.582771 27.582775 32.578246 24785.834
+Loop time of 606.774 on 1 procs for 10 steps with 2376 atoms
+
+Performance: 0.000 ns/day, 84274.222 hours/ns, 0.016 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 606.77 | 606.77 | 606.77 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00085855 | 0.00085855 | 0.00085855 | 0.0 | 0.00
+Output | 0.00087833 | 0.00087833 | 0.00087833 | 0.0 | 0.00
+Modify | 0.00041723 | 0.00041723 | 0.00041723 | 0.0 | 0.00
+Other | | 0.0001888 | | | 0.00
+
+Nlocal: 2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 13138 ave 13138 max 13138 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.96049e+06 ave 1.96049e+06 max 1.96049e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1960492
+Ave neighs/atom = 825.123
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:23:48
diff --git a/potentials/README b/potentials/README
index d4dba824c..357b9291c 100644
--- a/potentials/README
+++ b/potentials/README
@@ -1,103 +1,105 @@
This directory contains potential files for different elements and
alloys, as used by LAMMPS for various pair styles. See the
description of the "pair_style" and "pair_coeff" commands for details
of the file formats and the various styles in LAMMPS that read these
files.
IMPORTANT NOTE: These files are provided primarily to demonstrate the
different types of interatomic potentials that LAMMPS supports. Each
file has a header line with a date for when it was added to the LAMMPS
distribution. Also a citation and contact info for the person who
contributed it to LAMMPS (if we remember who that is). This info is
not meant to "guarantee" that the potential is correct. I.e. that the
contributor transcribed the info from the paper correctly or that the
paper itself had no errors. In many cases (but not all), we or other
LAMMPS users have confirmed that when the potential file is used with
the current version of LAMMPS, it reproduces results in the cited
publication. In some cases, this accuracy check may require other
parameters not contained in the potential file to be specified as part
of a LAMMPS simulation, e.g. a distance cutoff. Also, for particular
materials and applications modeled with a pair style coded in LAMMPS,
a different potential file may be more suitable than the one provided
here. For best results when choosing a potential, you should do a
thorough search of published literature and on-line databases such as
the Interatomic Potentials Repository Project (NIST) or the
Knowledgebase of Interatomic Models (KIM). Whatever potential you
choose for your application, you should verify that you have defined
it and are using it correctly in LAMMPS, by comparing with published
results for that potential.
2nd IMPORTANT NOTE: The DATE field in the first line of each of these
files is printed to the screen and log file when it is read by a
LAMMPS input script. If an updated or corrected version of the same
potential file is later added to the LAMMPS distribution, then a new
DATE will be added to the file. This means you can "diff" an old and
new log file and see that the potential file changed, which could
affect your simulation results.
A small amount of metadata is included in the first line of each file
in order to track the provenance of each file. The metadata is
indicated by a keyword followed by white space, followed by the
metadata, followed by whitespace. The metadata is intended to be
straightforward and human-readable, while still conforming to a
standard format.
DATE: Format is "yyyy-mm-dd". This indicates the date of a significant
change to the file. Multiple entries can appear in reverse
chronological order. As described above, the first of these will be
printed to the screen and log file when it is read by a LAMMPS input
script.
CONTRIBUTOR: Format is "name[, email address]". This indicates the person
who contributed the file and/or who is best able to provide more details
about its provenance.
CITATION: Format is "surname[[, surname] and surname], Publication
abbreviation with spaces and no periods, volume, page[-page], (year)"
COMMENT: This one is optional and is used to hold any other text that
can not go elsewhere.
If the first line of the file is always skipped by the file reader,
then the first line should begin with the DATE keyword. If the file
format supports comment lines, then the first line should be a comment
line with the metadata e.g. "# DATE: 2010-01-01..." If the first line
of the file is required to begin with data, then the metadata will be
appended to the first line e.g. "7 DATE: 2010-01-01..."
The prefix of each file indicates the element(s) it is parameterized
for. An additional lower-case identification tag may be appended.
Si = Silicon
SiC = Silicon and Carbon
Au_u3 = Gold universal 3
The suffix of each file indicates the pair style it is used with:
adp ADP angular dependent potential
airebo AI-REBO and REBO potentials
bop.table BOP potential, tabulated form
cdeam concentration-dependent EAM
comb COMB potential
comb3 COMB3 potential
eam embedded atom method (EAM) single element, DYNAMO funcfl format
eam.alloy EAM multi-element alloy, DYNAMO setfl format
eam.fs Finnis-Sinclair EAM format (single element or alloy)
edip EDIP potential for silicon-based materials
eim embedded-ion method (EIM) potential
lcbop LCBOP long-range bond-order potential
meam modified EAM (MEAM) library and individual elements/alloys
meam.spline modified EAM (MEAM) spline potential
meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
+mgpt model generalized pseudopotential theory (MGPT) potential
nb3b.harmonic nonbonded 3-body harmonic potential
poly polymorphic 3-body potential
reax ReaxFF potential (see README.reax for more info)
+smtbq second moment tight binding QEq (SMTBQ) potential
snap SNAP potential
snapcoeff SNAP potential
snapparam SNAP potential
streitz Coulombic portion of Streitz-Mintmire potential
sw Stillinger-Weber potential
tersoff Tersoff potential
tersoff.mod modified Tersoff potential
tersoff.zbl Tersoff with ZBL core
vashishta Vashishta 2-body and 3-body potential
diff --git a/potentials/ffield.smtbq.Al b/potentials/ffield.smtbq.Al
new file mode 100755
index 000000000..f63b6c43b
--- /dev/null
+++ b/potentials/ffield.smtbq.Al
@@ -0,0 +1,34 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# SMTBQ parameter for Al-Al interaction.
+# Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ.
+# year: 2014
+# =========================================================================
+' Nombre.de.type.d.atome..........:' 1
+' ====== atomic parameters ======= '
+' Cation.de.l.oxyde..Stoechio.....:' 'Al' 1
+' Qform.....masse.................:' 3.0 26.98
+' Param.QEq.(ne,.Chi,.J,.R_eff)...:' 3 1.19258 11.05345 0.57701
+' Nbre.d.etats.partage.par.cation.:' 3
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Al' 'Al' 'second_moment' 'metal'
+' Potentiel.Cat-Ox.(A,.p,.Ksi,.q).:' 0.1221 8.612 1.316 2.516
+' Pot..Cat-Ox.(rc1,.rc2,.r0).Iota.:' 5.6 7.0 2.863 2.0
+' ======== Parametre tab ========= '
+' Rcoul...........................:' 11.1714
+' rmin...dr.......................:' 1.18845 0.001
+' ======== IFQM Parameter ======== '
+' Frenquency.Q.resolution..........' 0
+' loopmax.-.precision..............' 5000 0.0002
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.5 3.2
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' 0.0
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAllParallel'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== END's parameters =========================
+
diff --git a/potentials/ffield.smtbq.Al2O3 b/potentials/ffield.smtbq.Al2O3
new file mode 100755
index 000000000..9c26ade9e
--- /dev/null
+++ b/potentials/ffield.smtbq.Al2O3
@@ -0,0 +1,56 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# SMTBQ parameter for AlO interaction with a limit length 'rc2sm=dc2**2'.
+# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ.
+#
+# Presentation atom : nature
+# q, qmin, qmax, masse
+# parameter QEq : Chi, J, R_eff
+# Parameter SM : A, p, Ksi, q
+# CutOff SM : dc1, dc2, r0
+# =========================================================================
+# -------------------------- Begin's parameters ---------------------------
+' Number.of.atoms.type............:' 2
+' ====== atomic parameters ======= '
+' 1st.element.(Oxygen).Stoechio...:' 'O' 3
+' Qform.....mass..................:' -2.0 16.00
+' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
+' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 4. 3.00 0.529 0.529 0.529
+' Number.of.shared.state.by.ions..:' 3
+' -------------------------------- '
+' 2nd.element.(metal).Stoechio....:' 'Al' 2
+' Qform.....mass..................:' 3.0 26.98
+' Param.QEq.(ne,.Chi0,.Ji0,.R_eff):' 3 1.19009 11.1903 0.56619
+' Number.of.shared.state.by.ions..:' 4
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Al' 'O' 'second_moment' 'oxide'
+' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.18176 8.80041 0.26044 1.58851
+' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 4. 5.6 1.91
+' -------------------------------- '
+' atom1..atom2..potential..........' 'O' 'O' 'buck'
+' Potentiel.O-O...(C,.Rho)........:' 580.440 0.3540
+' ======== Parametre tab ========= '
+' Rcoul=a*rc(SMASH)...............:' 11.1714
+' rmin...dr.......................:' 1.18845 0.001
+' ======== IFQM Parameter ======== '
+' Nevery.charge.calculation........' 1
+' loopmax....precision.............' 7000 0.000001
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.5 3.2
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' -1.8
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAll'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== FIN des parametres =========================
+
+#Possible QInit modes
+# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
+#any other name would lead to either 0 charges or charge read from the lammps atomic position file
+#Possible QEq modes | parameters
+# QEqAll | no parameters
+# QEqAllParallel | no parameters
+# Surface | zlim (QEq only for z>zlim)
diff --git a/potentials/ffield.smtbq.TiO2 b/potentials/ffield.smtbq.TiO2
new file mode 100755
index 000000000..4c8d9df53
--- /dev/null
+++ b/potentials/ffield.smtbq.TiO2
@@ -0,0 +1,53 @@
+# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+# ========================================================================
+# SMTBQ parameter for Ti-O interaction with a limit length 'rc2sm=dc2**2'.
+# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ
+# september 2014
+# ========================================================================
+' Number.of.atoms.type............:' 2
+' ====== atomic parameters ======= '
+' 1st.element.(Oxygen).Stoechio...:' 'O' 2
+' Qform.....mass..................:' -2.0 16.00
+' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
+' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 3. 2.00 0.52 0.54348 0.58
+' Number.of.shared.state.by.ions..:' 3
+' -------------------------------- '
+' 2nd.element.(metal).Stoechio....:' 'Ti' 1
+' Qform.....mass..................:' 4.0 26.98
+' Param.QEq.(nq,.Chi0,.Ji0,.R_eff):' 3 0.00 10.572 0.734
+' Number.of.shared.state.by.ions..:' 5
+' ===== potential Parameter ======'
+' Atom1..atom2..potential..mode....' 'Ti' 'O' 'second_moment' 'oxide'
+' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.134 12.609 0.5434 2.0965
+' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 3.6 6.0 1.95
+' -------------------------------- '
+' atom1..atom2..potential..........' 'O' 'O' 'buckPlusAttr'
+' Potential.O-O...(C,.Rho)........:' 580.440 0.3540
+' Potential.O-O...(D.B.r1OO.r2OO).:' -20.86 -0.916 1.4 1.8
+' ======== Tab Parameter ========= '
+' Rcoul=a*rc(SMASH)...............:' 12.1744
+' rmin...dr.......................:' 1.0675 0.001
+' ======== IFQM Parameter ======== '
+' Nevery.charge.calculation........' 1
+' loopmax....precision.............' 7000 0.000001
+' ==== Coordination parameters ===='
+' .r1n................r2n..........' 2.0 3.5
+' ========== QInitMode ========= '
+' QInitMode....QInit(if.needed)....' 'false' -1.0
+' ======== Mode for QEq ======== '
+' mode(see.end.of.this.file.)......' 'QEqAll'
+' parameters.for.mode..............'
+' ========== Verbose ============ '
+' Verbose(true.or.false)...........' 'false'
+' Print.Energy.components..........' 'false' 300.0
+' Print.electroneg...components....' 'false' 300.0
+# =========================== END's parameters =========================
+
+#Possible QInit modes
+# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
+#any other name would lead to either 0 charges or charge read from the lammps atomic position file
+#Possible QEq modes | parameters
+# QEqAll | no parameters
+# QEqAllParallel | no parameters
+# Surface | zlim (QEq only for z>zlim)
+# BulkFromSlab | zlim1 zlim2 (QEq only for zlim1<z<zlim2)
diff --git a/src/Makefile b/src/Makefile
index 3a3eb207a..982bdb087 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,323 +1,323 @@
# LAMMPS multiple-machine -*- Makefile -*-
SHELL = /bin/bash
#.IGNORE:
# Definitions
ROOT = lmp
EXE = lmp_$@
ARLIB = liblammps_$@.a
SHLIB = liblammps_$@.so
ARLINK = liblammps.a
SHLINK = liblammps.so
OBJDIR = Obj_$@
OBJSHDIR = Obj_shared_$@
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
OBJ = $(SRC:.cpp=.o)
SRCLIB = $(filter-out main.cpp,$(SRC))
OBJLIB = $(filter-out main.o,$(OBJ))
# Command-line options for mode: exe (default), shexe, lib, shlib
mode = exe
objdir = $(OBJDIR)
ifeq ($(mode),shexe)
objdir = $(OBJSHDIR)
endif
ifeq ($(mode),lib)
objdir = $(OBJDIR)
endif
ifeq ($(mode),shlib)
objdir = $(OBJSHDIR)
endif
# Package variables
PACKAGE = asphere body class2 colloid compress coreshell dipole fld gpu \
granular kim kokkos kspace manybody mc meam misc molecule mpiio \
opt peri poems python qeq replica rigid shock snap srd \
voronoi xtc
PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
user-diffraction user-drude user-eff user-fep user-h5md \
- user-intel user-lb user-misc user-molfile user-omp user-phonon \
- user-qmmm user-qtb user-quip user-reaxc user-smd user-sph \
- user-tally
+ user-intel user-lb user-mgpt \
+ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
+ user-quip user-reaxc user-smd user-smtbq user-sph user-tally
PACKLIB = compress gpu kim kokkos meam mpiio poems python voronoi \
user-atc user-awpmd user-colvars user-cuda user-h5md user-intel \
user-lb user-molfile user-qmmm user-quip user-smd
PACKALL = $(PACKAGE) $(PACKUSER)
PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)
YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
NODIR = $(shell echo $(@:no-%=%) | tr a-z A-Z)
# List of all targets
help:
@echo ''
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
@echo 'make mpi-stubs build dummy MPI library in STUBS'
@echo 'make install-python install LAMMPS wrapper in Python'
@echo 'make tar create lmp_src.tar.gz of src dir and packages'
@echo ''
@echo 'make package list available packages'
@echo 'make package-status (ps) status of all packages'
@echo 'make yes-package install a single pgk in src dir'
@echo 'make no-package remove a single pkg from src dir'
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
@echo 'make no-standard (no-std) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make no-lib remove all pkgs with external libs'
@echo ''
@echo 'make package-update (pu) replace src files with updated package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package files'
@echo 'make package-purge purge obsolete copies of package sources'
@echo ''
@echo 'make machine build LAMMPS for machine'
@echo 'make mode=lib machine build LAMMPS as static lib for machine'
@echo 'make mode=shlib machine build LAMMPS as shared lib for machine'
@echo 'make mode=shexe machine build LAMMPS as shared exe for machine'
@echo 'make makelist create Makefile.list used by old makes'
@echo 'make -f Makefile.list machine build LAMMPS for machine (old)'
@echo ''
@echo 'machine is one of these from src/MAKE:'
@echo ''
@files="`ls MAKE/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/OPTIONS:'
@echo ''
@files="`ls MAKE/OPTIONS/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/MACHINES:'
@echo ''
@files="`ls MAKE/MACHINES/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/MINE:'
@echo ''
@files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \
for file in $$files; do head -1 $$file; done
@echo ''
# Build LAMMPS in one of 4 modes
# exe = exe with static compile in Obj_machine (default)
# shexe = exe with shared compile in Obj_shared_machine
# lib = static lib in Obj_machine
# shlib = shared lib in Obj_shared_machine
.DEFAULT:
@if [ $@ = "serial" -a ! -f STUBS/libmpi_stubs.a ]; \
then $(MAKE) mpi-stubs; fi
@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
-f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@
@if [ ! -d $(objdir) ]; then mkdir $(objdir); fi
@$(SHELL) Make.sh style
@if [ -f MAKE/MACHINES/Makefile.$@ ]; \
then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/OPTIONS/Makefile.$@ ]; \
then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/Makefile.$@ ]; \
then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/MINE/Makefile.$@ ]; \
then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi
@if [ ! -e Makefile.package ]; \
then cp Makefile.package.empty Makefile.package; fi
@if [ ! -e Makefile.package.settings ]; \
then cp Makefile.package.settings.empty Makefile.package.settings; fi
@cp Makefile.package Makefile.package.settings $(objdir)
ifeq ($(mode),exe)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "SHFLAGS =" \
"EXE = ../$(EXE)" ../$(EXE)
endif
ifeq ($(mode),shexe)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" \
"EXE = ../$(EXE)" ../$(EXE)
endif
ifeq ($(mode),lib)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \
"EXE = ../$(ARLIB)" lib
@rm -f $(ARLINK)
@ln -s $(ARLIB) $(ARLINK)
endif
ifeq ($(mode),shlib)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \
"EXE = ../$(SHLIB)" shlib
@rm -f $(SHLINK)
@ln -s $(SHLIB) $(SHLINK)
endif
# Remove machine-specific object files
clean:
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
clean-all:
rm -rf Obj_*
clean-%:
rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%)
test-clean:
@cd ../test/; $(MAKE) $(MFLAGS) clean; cd ..
test-%:
$(MAKE) $(MFLAGS) $(@:test-%=%)
@cd ../test/; $(MAKE) $(MFLAGS) test MACH=$(@:test-%=%) MPICMD="$(MPICMD)" LMPFLAGS="$(LMPFLAGS)" TAG=$(TAG) || exit 1 ; cd ..
# Create Makefile.list
makelist:
@$(SHELL) Make.sh style
@$(SHELL) Make.sh Makefile.list
# Make MPI STUBS library
mpi-stubs:
@cd STUBS; $(MAKE) clean; $(MAKE)
# install LAMMPS shared lib and Python wrapper for Python usage
install-python:
@python ../python/install.py
# Create a tarball of src dir and packages
tar:
@cd STUBS; $(MAKE) clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/MAKE src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn
@cd STUBS; $(MAKE)
@echo "Created $(ROOT)_src.tar.gz"
# Package management
package:
@echo 'Standard packages:' $(PACKAGE)
@echo ''
@echo 'User-contributed packages:' $(PACKUSER)
@echo ''
@echo 'make package list available packages'
@echo 'make package-status (ps) status of all packages'
@echo 'make yes-package install a single pgk in src dir'
@echo 'make no-package remove a single pkg from src dir'
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
@echo 'make no-standard (no-srd) remove all standard pkgs'
@echo ''
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make no-lib remove all pkgs with external libs'
@echo 'make package-update (pu) replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package file'
yes-all:
@for p in $(PACKALL); do $(MAKE) yes-$$p; done
no-all:
@for p in $(PACKALL); do $(MAKE) no-$$p; done
yes-standard yes-std:
@for p in $(PACKAGE); do $(MAKE) yes-$$p; done
no-standard no-std:
@for p in $(PACKAGE); do $(MAKE) no-$$p; done
yes-user:
@for p in $(PACKUSER); do $(MAKE) yes-$$p; done
no-user:
@for p in $(PACKUSER); do $(MAKE) no-$$p; done
no-lib:
@for p in $(PACKLIB); do $(MAKE) no-$$p; done
yes-%:
@if [ ! -e Makefile.package ]; \
then cp Makefile.package.empty Makefile.package; fi
@if [ ! -e Makefile.package.settings ]; \
then cp Makefile.package.settings.empty Makefile.package.settings; fi
@if [ ! -e $(YESDIR) ]; then \
echo "Package $(@:yes-%=%) does not exist"; \
elif [ -e $(YESDIR)/Install.sh ]; then \
echo "Installing package $(@:yes-%=%)"; \
cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \
$(SHELL) Depend.sh $(YESDIR) 1; \
else \
echo "Installing package $(@:yes-%=%)"; \
cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \
$(SHELL) Depend.sh $(YESDIR) 1; \
fi;
no-%:
@if [ ! -e $(NODIR) ]; then \
echo "Package $(@:no-%=%) does not exist"; \
elif [ -e $(NODIR)/Install.sh ]; then \
echo "Uninstalling package $(@:no-%=%)"; \
cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \
$(SHELL) Depend.sh $(NODIR) 0; \
else \
echo "Uninstalling package $(@:no-%=%)"; \
cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \
$(SHELL) Depend.sh $(NODIR) 0; \
fi;
# status = list src files that differ from package files
# update = replace src files with newer package files
# overwrite = overwrite package files with newer src files
# diff = show differences between src and package files
# purge = delete obsolete and auto-generated package files
package-status ps:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done
package-update pu:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done
package-overwrite:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done
package-diff pd:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done
package-purge: Purge.list
@echo 'Purging obsolete and auto-generated source files'
@for f in `grep -v '#' Purge.list` ; \
do test -f $$f && rm $$f && echo $$f || : ; \
done
diff --git a/src/USER-MGPT/README b/src/USER-MGPT/README
new file mode 100644
index 000000000..dac08c5f0
--- /dev/null
+++ b/src/USER-MGPT/README
@@ -0,0 +1,33 @@
+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 the doc page for the pair_style mgpt command for full details on
+using this package in LAMMPS. In particular, the user should note that
+the MGPT potentials are explicitly volume dependent, requiring special
+attention in their application. Useful example scripts are given in
+the "examples/USER/mgpt" directory. These scripts show the necessary
+steps to perform constant-volume calculations and simulations. It is
+strongly recommended that the user work through and understand these
+examples before proceeding to more complex simulations.
+
+Specific MGPT potential data for the transition metals tantalum
+(Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and
+vanadium (V6.1 potentials) are contained in the LAMMPS "potentials"
+directory. It is expected that MGPT potentials for additional
+materials will be added over time.
+
+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.
diff --git a/src/USER-MGPT/mgpt_bgmul_7.c.h b/src/USER-MGPT/mgpt_bgmul_7.c.h
new file mode 100644
index 000000000..d4e87c9fe
--- /dev/null
+++ b/src/USER-MGPT/mgpt_bgmul_7.c.h
@@ -0,0 +1,181 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+
+//#define TESTING
+
+#ifdef TESTING
+
+typedef struct {
+ double x,y;
+} pair;
+
+
+#define CPLX pair
+
+#define __creal my_creal
+#define __cimag my_cimag
+#define __lfpd my_lfpd
+#define __stfpd my_stfpd
+#define __fxsmul my_fxsmul
+#define __fxcpmadd my_fxcpmadd
+
+#else
+
+#define CPLX double _Complex
+
+#endif
+
+static double my_creal(CPLX x) {
+ return ((double *) &x)[0];
+}
+static double my_cimag(CPLX x) {
+ return ((double *) &x)[1];
+}
+static CPLX my_lfpd(const double *p) {
+ return ((CPLX *) p)[0];
+}
+static void my_stfpd(double *p,CPLX x) {
+ ((CPLX *) p)[0] = x;
+}
+static CPLX my_fxsmul(CPLX x,double a) {
+ double y[2];
+ y[0] = a * my_creal(x);
+ y[1] = a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) {
+ double y[2];
+ y[0] = my_creal(t) + a * my_creal(x);
+ y[1] = my_cimag(t) + a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+
+void bgmul_7(double (* restrict Ain)[8],double (* restrict Bin)[8],double (* restrict Cin)[8]) {
+
+CPLX C1,C2,C3,C4,C5,C6,C7;
+CPLX A1_01,A1_23,A1_45,A1_67;
+CPLX A2_23,A2_45,A2_67;
+CPLX A3_23,A3_45,A3_67;
+CPLX A4_45,A4_67;
+CPLX A5_45,A5_67;
+CPLX A6_67;
+CPLX A7_67;
+CPLX Bkj;
+
+ double (* restrict A)[8] = &Ain[-1];
+ double (* restrict B)[8] = &Bin[-1];
+ double (* restrict C)[8] = &Cin[-1];
+
+
+int j;
+A1_01 = __lfpd(&A[1][0]); A1_23 = __lfpd(&A[1][2]); A1_45 = __lfpd(&A[1][4]); A1_67 = __lfpd(&A[1][6]);
+ A2_23 = __lfpd(&A[2][2]); A2_45 = __lfpd(&A[2][4]); A2_67 = __lfpd(&A[2][6]);
+ A3_23 = __lfpd(&A[3][2]); A3_45 = __lfpd(&A[3][4]); A3_67 = __lfpd(&A[3][6]);
+ A4_45 = __lfpd(&A[4][4]); A4_67 = __lfpd(&A[4][6]);
+ A5_45 = __lfpd(&A[5][4]); A5_67 = __lfpd(&A[5][6]);
+ A6_67 = __lfpd(&A[6][6]);
+ A7_67 = __lfpd(&A[7][6]);
+
+for(j = 0; j<7; j+=2) {
+ /* k = 1 */
+ Bkj = __lfpd(&B[1][j]);
+
+ C1 = __fxsmul(Bkj,__cimag(A1_01));
+ C2 = __fxsmul(Bkj,__creal(A1_23));
+ C3 = __fxsmul(Bkj,__cimag(A1_23));
+ C4 = __fxsmul(Bkj,__creal(A1_45));
+ C5 = __fxsmul(Bkj,__cimag(A1_45));
+ C6 = __fxsmul(Bkj,__creal(A1_67));
+ C7 = __fxsmul(Bkj,__cimag(A1_67));
+
+ /* k = 2 */
+ Bkj = __lfpd(&B[2][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__creal(A1_23));
+ C2 = __fxcpmadd(C2,Bkj,__creal(A2_23));
+ C3 = __fxcpmadd(C3,Bkj,__cimag(A2_23));
+ C4 = __fxcpmadd(C4,Bkj,__creal(A2_45));
+ C5 = __fxcpmadd(C5,Bkj,__cimag(A2_45));
+ C6 = __fxcpmadd(C6,Bkj,__creal(A2_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A2_67));
+
+ /* k = 3 */
+ Bkj = __lfpd(&B[3][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__cimag(A1_23));
+ C2 = __fxcpmadd(C2,Bkj,__cimag(A2_23));
+ C3 = __fxcpmadd(C3,Bkj,__cimag(A3_23));
+ C4 = __fxcpmadd(C4,Bkj,__creal(A3_45));
+ C5 = __fxcpmadd(C5,Bkj,__cimag(A3_45));
+ C6 = __fxcpmadd(C6,Bkj,__creal(A3_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A3_67));
+
+ /* k = 4 */
+ Bkj = __lfpd(&B[4][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__creal(A1_45));
+ C2 = __fxcpmadd(C2,Bkj,__creal(A2_45));
+ C3 = __fxcpmadd(C3,Bkj,__creal(A3_45));
+ C4 = __fxcpmadd(C4,Bkj,__creal(A4_45));
+ C5 = __fxcpmadd(C5,Bkj,__cimag(A4_45));
+ C6 = __fxcpmadd(C6,Bkj,__creal(A4_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A4_67));
+
+ /* k = 5 */
+ Bkj = __lfpd(&B[5][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__cimag(A1_45));
+ C2 = __fxcpmadd(C2,Bkj,__cimag(A2_45));
+ C3 = __fxcpmadd(C3,Bkj,__cimag(A3_45));
+ C4 = __fxcpmadd(C4,Bkj,__cimag(A4_45));
+ C5 = __fxcpmadd(C5,Bkj,__cimag(A5_45));
+ C6 = __fxcpmadd(C6,Bkj,__creal(A5_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A5_67));
+
+ /* k = 6 */
+ Bkj = __lfpd(&B[6][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__creal(A1_67));
+ C2 = __fxcpmadd(C2,Bkj,__creal(A2_67));
+ C3 = __fxcpmadd(C3,Bkj,__creal(A3_67));
+ C4 = __fxcpmadd(C4,Bkj,__creal(A4_67));
+ C5 = __fxcpmadd(C5,Bkj,__creal(A5_67));
+ C6 = __fxcpmadd(C6,Bkj,__creal(A6_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A6_67));
+
+ /* k = 7 */
+ Bkj = __lfpd(&B[7][j]);
+
+ C1 = __fxcpmadd(C1,Bkj,__cimag(A1_67));
+ C2 = __fxcpmadd(C2,Bkj,__cimag(A2_67));
+ C3 = __fxcpmadd(C3,Bkj,__cimag(A3_67));
+ C4 = __fxcpmadd(C4,Bkj,__cimag(A4_67));
+ C5 = __fxcpmadd(C5,Bkj,__cimag(A5_67));
+ C6 = __fxcpmadd(C6,Bkj,__cimag(A6_67));
+ C7 = __fxcpmadd(C7,Bkj,__cimag(A7_67));
+
+ __stfpd(&C[1][j],C1);
+ __stfpd(&C[2][j],C2);
+ __stfpd(&C[3][j],C3);
+ __stfpd(&C[4][j],C4);
+ __stfpd(&C[5][j],C5);
+ __stfpd(&C[6][j],C6);
+ __stfpd(&C[7][j],C7);
+}
+}
diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp
new file mode 100644
index 000000000..185b61e1c
--- /dev/null
+++ b/src/USER-MGPT/mgpt_linalg.cpp
@@ -0,0 +1,203 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include "mgpt_linalg.h"
+
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
+#include <cassert>
+
+#define restrict __restrict__
+
+#ifdef IBM_BG_SIMD
+#include <builtins.h>
+
+/* Double precision 440d (double hummer) matrix multiplication */
+#define const
+#include "mgpt_mmul_bg_552.c.h"
+#include "mgpt_mmul_bg_722.c.h"
+#include "mgpt_bgmul_7.c.h"
+
+/* Double precision 440d (double hummer) product trace */
+#define real double
+#include "mgpt_ttr_5123.c.h"
+#include "mgpt_ttr_7123.c.h"
+#undef real
+#undef const
+#endif
+
+
+#ifdef IBM_BGQ_SIMD
+/* Double precision QPX matrix multiplication */
+#include "mgpt_mmul_bgq_n5_lda8_2x8.c.h"
+#include "mgpt_mmul_bgq_n7_lda8_4x8.c.h"
+
+/* Double precision QPX product trace */
+#include "mgpt_ttr_5141.c.h"
+#include "mgpt_ttr_7141.c.h"
+#endif
+
+
+#ifdef x86_SIMD
+/* Double precision SSE2 matrix multiplication */
+#include "mgpt_mmul3d_526.c.h"
+#include "mgpt_mmul3d_744.c.h"
+
+/* Single precision SSE2 matrix multiplication */
+#include "mgpt_mmul3_538.c.h"
+#include "mgpt_mmul3_748.c.h"
+
+/* Double precision SSE3 product trace */
+#define real double
+#include "mgpt_ttr_5022.c.h"
+#include "mgpt_ttr_7022.c.h"
+#undef real
+
+/* Single precision SSE3 product trace */
+#define real float
+#include "mgpt_ttr_5042.c.h"
+#include "mgpt_ttr_7042.c.h"
+#undef real
+
+#endif
+
+#if defined(IBM_BG_SIMD) || defined(IBM_BGQ_SIMD)
+#define const
+#endif
+static void transprod_generic(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ const int lda = 8,n = mgpt_linalg::matrix_size;
+ int i,j,k;
+ double s;
+ for(i = 0; i<n; i++)
+ for(j = 0; j<n; j++) {
+ s = 0.0;
+ for(k = 1; k<=n; k++)
+ s = s + A[i*lda+k]*B[j*lda+k];
+ C[i*lda+(j+1)] = s;
+ }
+}
+
+static void transtrace3_generic(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+ const int lda = 8,n = mgpt_linalg::matrix_size;
+ double t0 = 0.0,t1 = 0.0,t2 = 0.0;
+ int i,j;
+
+ for(i = 0; i<n; i++)
+ for(j = 1; j<=n; j++) {
+ int idx = i*lda + j;
+ double atmp = A[idx];
+ t0 = t0 + atmp*B0[idx];
+ t1 = t1 + atmp*B1[idx];
+ t2 = t2 + atmp*B2[idx];
+ }
+ *tout0 = t0;
+ *tout1 = t1;
+ *tout2 = t2;
+}
+
+static void transprod_error(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ printf("Linear algebra subroutines not initialized (transprod).\n");
+ exit(1);
+}
+static void transtrace3_error(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+ printf("Linear algebra subroutines not initialized (transtrace3).\n");
+ exit(1);
+}
+
+
+#if defined(IBM_BG_SIMD) || defined(IBM_BGQ_SIMD)
+#undef const
+#endif
+
+#undef restrict
+
+int mgpt_linalg::matrix_size;
+
+mgpt_linalg::mgpt_linalg() {
+ mgpt_linalg::matrix_size = 0;
+
+ tr_mul = transprod_error;
+ tr_trace = transtrace3_error;
+ single = 0;
+}
+
+mgpt_linalg::mgpt_linalg(int n,int single_precision) {
+
+ mgpt_linalg::matrix_size = n;
+
+ tr_mul = transprod_generic;
+ tr_trace = transtrace3_generic;
+ single = 0;
+ msg = "@@@ Choosing generic (unoptimized) linear algebra routines.\n";
+
+#ifdef IBM_BG_SIMD
+ msg = "@@@ Choosing BG/L optimized linear algebra routines.\n";
+ if(n == 5) {
+ tr_mul = mmul_bg_5_8_5x2v2;
+ tr_trace = ttr_bg_5_8_3_v2r3;
+ } else if(n == 7) {
+ //tr_mul = mmul_bg_7_8_2x2v2;
+ tr_mul = (trmul_fun) bgmul_7;
+ tr_trace = ttr_bg_7_8_3_v2r3;
+ }
+#elif defined(IBM_BGQ_SIMD)
+ msg = "@@@ Choosing BG/Q optimized linear algebra routines.\n";
+ if(1) {
+ if(n == 5) {
+ tr_mul = mmul_bgq_n5_lda8_2x8;
+ tr_trace = ttr_bg_5_8_3_v4r1;
+ } else if(n == 7) {
+ tr_mul = mmul_bgq_n7_lda8_4x8;
+ tr_trace = ttr_bg_7_8_3_v4r1;
+ }
+ }
+#elif defined(x86_SIMD)
+ if(single_precision) {
+ msg = "@@@ Choosing Intel/AMD single precision linear algebra routines.\n";
+ if(n == 5) {
+ tr_mul = (trmul_fun) mmul3_5_8_3x8v4;
+ tr_trace = (trtrace3_fun) ttr_5_8_3_v4r2;
+ single = 1;
+ } else if(n == 7) {
+ tr_mul = (trmul_fun) mmul3_7_8_4x8v4;
+ tr_trace = (trtrace3_fun) ttr_7_8_3_v4r2;
+ single = 1;
+ }
+ } else {
+ msg = "@@@ Choosing Intel/AMD double precision linear algebra routines.\n";
+ if(n == 5) {
+ tr_mul = mmul3_5_8_2x6v2;
+ tr_trace = ttr_5_8_3_v2r2;
+ } else if(n == 7) {
+ tr_mul = mmul3_7_8_4x4v2;
+ tr_trace = ttr_7_8_3_v2r2;
+ }
+ }
+#endif
+}
diff --git a/src/USER-MGPT/mgpt_linalg.h b/src/USER-MGPT/mgpt_linalg.h
new file mode 100644
index 000000000..a22956a7f
--- /dev/null
+++ b/src/USER-MGPT/mgpt_linalg.h
@@ -0,0 +1,69 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#ifndef MGPT_LINALG__
+#define MGPT_LINALG__
+
+
+#ifdef __bg__
+
+ #ifdef __bgq__
+ #ifdef __VECTOR4DOUBLE__
+ #define IBM_BGQ_SIMD
+ #endif
+ #else
+ #define IBM_BG_SIMD
+ #endif
+
+#elif defined(__SSE3__)
+ #define x86_SIMD
+#endif
+
+#define restrict __restrict__
+
+#if defined(IBM_BG_SIMD) || defined(IBM_BGQ_SIMD)
+#define const
+#endif
+typedef void (*trmul_fun) (const double * restrict A,
+ const double * restrict B,
+ double * restrict C);
+
+typedef void (*trtrace3_fun) (const double * restrict A,
+ const double * restrict B1,double * restrict t1,
+ const double * restrict B2,double * restrict t2,
+ const double * restrict B3,double * restrict t3);
+#if defined(IBM_BG_SIMD) || defined(IBM_BGQ_SIMD)
+#undef const
+#endif
+
+class mgpt_linalg {
+ public:
+ static int matrix_size;
+
+ trmul_fun tr_mul;
+ trtrace3_fun tr_trace;
+ int single;
+ const char *msg;
+
+ mgpt_linalg();
+ mgpt_linalg(int n,int single_precision);
+};
+
+#undef restrict
+
+#endif
diff --git a/src/USER-MGPT/mgpt_mmul3_538.c.h b/src/USER-MGPT/mgpt_mmul3_538.c.h
new file mode 100644
index 000000000..f47059099
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul3_538.c.h
@@ -0,0 +1,295 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+void mmul3_5_8_3x8v4(const float * restrict A,
+ const float * restrict B,
+ float * restrict C) {
+ __m128
+ Creg00,Creg04,
+ Creg10,Creg14,
+ Creg20,Creg24;
+ __m128 Areg0,Areg1,Areg2;
+ __m128 Breg0,Breg4;
+ __m128 Atmp,Btmp;
+
+
+ /* Computing C(0:2,0:5) */
+
+ Areg0 = _mm_load_ps(&A[0]) ;
+ Areg1 = _mm_load_ps(&A[8]) ;
+ Areg2 = _mm_load_ps(&A[16]) ;
+
+ Breg0 = _mm_load_ps(&B[0]) ;
+ Breg4 = _mm_load_ps(&B[4]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_ps(Creg00,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_ps(Creg04,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_ps(Creg10,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_ps(Creg14,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_ps(Creg20,Atmp) ;
+ Creg24 = Breg4 ;
+ Creg24 = _mm_mul_ps(Creg24,Atmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[8]) ;
+ Breg4 = _mm_load_ps(&B[12]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[16]) ;
+ Breg4 = _mm_load_ps(&B[20]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Areg0 = _mm_load_ps(&A[4]) ;
+ Areg1 = _mm_load_ps(&A[12]) ;
+ Areg2 = _mm_load_ps(&A[20]) ;
+
+ Breg0 = _mm_load_ps(&B[24]) ;
+ Breg4 = _mm_load_ps(&B[28]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[32]) ;
+ Breg4 = _mm_load_ps(&B[36]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ _mm_store_ps(&C[0],Creg00) ;
+ _mm_store_ps(&C[4],Creg04) ;
+ _mm_store_ps(&C[8],Creg10) ;
+ _mm_store_ps(&C[12],Creg14) ;
+ _mm_store_ps(&C[16],Creg20) ;
+ _mm_store_ps(&C[20],Creg24) ;
+
+
+ /* Computing C(3:4,0:5) */
+
+ Areg0 = _mm_load_ps(&A[24]) ;
+ Areg1 = _mm_load_ps(&A[32]) ;
+
+ Breg0 = _mm_load_ps(&B[0]) ;
+ Breg4 = _mm_load_ps(&B[4]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_ps(Creg00,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_ps(Creg04,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_ps(Creg10,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_ps(Creg14,Atmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[8]) ;
+ Breg4 = _mm_load_ps(&B[12]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[16]) ;
+ Breg4 = _mm_load_ps(&B[20]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+
+ Areg0 = _mm_load_ps(&A[28]) ;
+ Areg1 = _mm_load_ps(&A[36]) ;
+
+ Breg0 = _mm_load_ps(&B[24]) ;
+ Breg4 = _mm_load_ps(&B[28]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[32]) ;
+ Breg4 = _mm_load_ps(&B[36]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+
+ _mm_store_ps(&C[24],Creg00) ;
+ _mm_store_ps(&C[28],Creg04) ;
+ _mm_store_ps(&C[32],Creg10) ;
+ _mm_store_ps(&C[36],Creg14) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul3_748.c.h b/src/USER-MGPT/mgpt_mmul3_748.c.h
new file mode 100644
index 000000000..298fe753c
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul3_748.c.h
@@ -0,0 +1,508 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+void mmul3_7_8_4x8v4(const float * restrict A,
+ const float * restrict B,
+ float * restrict C) {
+ __m128
+ Creg00,Creg04,
+ Creg10,Creg14,
+ Creg20,Creg24,
+ Creg30,Creg34;
+ __m128 Areg0,Areg1,Areg2,Areg3;
+ __m128 Breg0,Breg4;
+ __m128 Atmp,Btmp;
+
+
+ /* Computing C(0:3,0:7) */
+
+ Areg0 = _mm_load_ps(&A[0]) ;
+ Areg1 = _mm_load_ps(&A[8]) ;
+ Areg2 = _mm_load_ps(&A[16]) ;
+ Areg3 = _mm_load_ps(&A[24]) ;
+
+ Breg0 = _mm_load_ps(&B[0]) ;
+ Breg4 = _mm_load_ps(&B[4]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_ps(Creg00,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_ps(Creg04,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_ps(Creg10,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_ps(Creg14,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_ps(Creg20,Atmp) ;
+ Creg24 = Breg4 ;
+ Creg24 = _mm_mul_ps(Creg24,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg30 = Breg0 ;
+ Creg30 = _mm_mul_ps(Creg30,Atmp) ;
+ Creg34 = Breg4 ;
+ Creg34 = _mm_mul_ps(Creg34,Atmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[8]) ;
+ Breg4 = _mm_load_ps(&B[12]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[16]) ;
+ Breg4 = _mm_load_ps(&B[20]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ Areg0 = _mm_load_ps(&A[4]) ;
+ Areg1 = _mm_load_ps(&A[12]) ;
+ Areg2 = _mm_load_ps(&A[20]) ;
+ Areg3 = _mm_load_ps(&A[28]) ;
+
+ Breg0 = _mm_load_ps(&B[24]) ;
+ Breg4 = _mm_load_ps(&B[28]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[32]) ;
+ Breg4 = _mm_load_ps(&B[36]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[40]) ;
+ Breg4 = _mm_load_ps(&B[44]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[48]) ;
+ Breg4 = _mm_load_ps(&B[52]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg30 = _mm_add_ps(Creg30,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg34 = _mm_add_ps(Creg34,Btmp) ;
+
+
+ _mm_store_ps(&C[0],Creg00) ;
+ _mm_store_ps(&C[4],Creg04) ;
+ _mm_store_ps(&C[8],Creg10) ;
+ _mm_store_ps(&C[12],Creg14) ;
+ _mm_store_ps(&C[16],Creg20) ;
+ _mm_store_ps(&C[20],Creg24) ;
+ _mm_store_ps(&C[24],Creg30) ;
+ _mm_store_ps(&C[28],Creg34) ;
+
+
+ /* Computing C(4:6,0:7) */
+
+ Areg0 = _mm_load_ps(&A[32]) ;
+ Areg1 = _mm_load_ps(&A[40]) ;
+ Areg2 = _mm_load_ps(&A[48]) ;
+
+ Breg0 = _mm_load_ps(&B[0]) ;
+ Breg4 = _mm_load_ps(&B[4]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_ps(Creg00,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_ps(Creg04,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_ps(Creg10,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_ps(Creg14,Atmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_ps(Creg20,Atmp) ;
+ Creg24 = Breg4 ;
+ Creg24 = _mm_mul_ps(Creg24,Atmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[8]) ;
+ Breg4 = _mm_load_ps(&B[12]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[16]) ;
+ Breg4 = _mm_load_ps(&B[20]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Areg0 = _mm_load_ps(&A[36]) ;
+ Areg1 = _mm_load_ps(&A[44]) ;
+ Areg2 = _mm_load_ps(&A[52]) ;
+
+ Breg0 = _mm_load_ps(&B[24]) ;
+ Breg4 = _mm_load_ps(&B[28]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[32]) ;
+ Breg4 = _mm_load_ps(&B[36]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[40]) ;
+ Breg4 = _mm_load_ps(&B[44]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ Breg0 = _mm_load_ps(&B[48]) ;
+ Breg4 = _mm_load_ps(&B[52]) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg00 = _mm_add_ps(Creg00,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg04 = _mm_add_ps(Creg04,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg10 = _mm_add_ps(Creg10,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg14 = _mm_add_ps(Creg14,Btmp) ;
+
+ Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg20 = _mm_add_ps(Creg20,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_ps(Btmp,Atmp) ;
+ Creg24 = _mm_add_ps(Creg24,Btmp) ;
+
+
+ _mm_store_ps(&C[32],Creg00) ;
+ _mm_store_ps(&C[36],Creg04) ;
+ _mm_store_ps(&C[40],Creg10) ;
+ _mm_store_ps(&C[44],Creg14) ;
+ _mm_store_ps(&C[48],Creg20) ;
+ _mm_store_ps(&C[52],Creg24) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul3d_526.c.h b/src/USER-MGPT/mgpt_mmul3d_526.c.h
new file mode 100644
index 000000000..47a4c26a2
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul3d_526.c.h
@@ -0,0 +1,443 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+void mmul3_5_8_2x6v2(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ __m128d
+ Creg00,Creg02,Creg04,
+ Creg10,Creg12,Creg14;
+ __m128d Areg0,Areg1;
+ __m128d Breg0,Breg2,Breg4;
+ __m128d Atmp,Btmp;
+
+
+ /* Computing C(0:1,0:5) */
+
+ Areg0 = _mm_load_pd(&A[0]) ;
+ Areg1 = _mm_load_pd(&A[8]) ;
+
+ Breg0 = _mm_load_pd(&B[0]) ;
+ Breg2 = _mm_load_pd(&B[2]) ;
+ Breg4 = _mm_load_pd(&B[4]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_pd(Creg04,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_pd(Creg14,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[2]) ;
+ Areg1 = _mm_load_pd(&A[10]) ;
+
+ Breg0 = _mm_load_pd(&B[8]) ;
+ Breg2 = _mm_load_pd(&B[10]) ;
+ Breg4 = _mm_load_pd(&B[12]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[16]) ;
+ Breg2 = _mm_load_pd(&B[18]) ;
+ Breg4 = _mm_load_pd(&B[20]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[4]) ;
+ Areg1 = _mm_load_pd(&A[12]) ;
+
+ Breg0 = _mm_load_pd(&B[24]) ;
+ Breg2 = _mm_load_pd(&B[26]) ;
+ Breg4 = _mm_load_pd(&B[28]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[32]) ;
+ Breg2 = _mm_load_pd(&B[34]) ;
+ Breg4 = _mm_load_pd(&B[36]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ _mm_store_pd(&C[0],Creg00) ;
+ _mm_store_pd(&C[2],Creg02) ;
+ _mm_store_pd(&C[4],Creg04) ;
+ _mm_store_pd(&C[8],Creg10) ;
+ _mm_store_pd(&C[10],Creg12) ;
+ _mm_store_pd(&C[12],Creg14) ;
+
+
+ /* Computing C(2:3,0:5) */
+
+ Areg0 = _mm_load_pd(&A[16]) ;
+ Areg1 = _mm_load_pd(&A[24]) ;
+
+ Breg0 = _mm_load_pd(&B[0]) ;
+ Breg2 = _mm_load_pd(&B[2]) ;
+ Breg4 = _mm_load_pd(&B[4]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_pd(Creg04,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+ Creg14 = Breg4 ;
+ Creg14 = _mm_mul_pd(Creg14,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[18]) ;
+ Areg1 = _mm_load_pd(&A[26]) ;
+
+ Breg0 = _mm_load_pd(&B[8]) ;
+ Breg2 = _mm_load_pd(&B[10]) ;
+ Breg4 = _mm_load_pd(&B[12]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[16]) ;
+ Breg2 = _mm_load_pd(&B[18]) ;
+ Breg4 = _mm_load_pd(&B[20]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[20]) ;
+ Areg1 = _mm_load_pd(&A[28]) ;
+
+ Breg0 = _mm_load_pd(&B[24]) ;
+ Breg2 = _mm_load_pd(&B[26]) ;
+ Breg4 = _mm_load_pd(&B[28]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[32]) ;
+ Breg2 = _mm_load_pd(&B[34]) ;
+ Breg4 = _mm_load_pd(&B[36]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg14 = _mm_add_pd(Creg14,Btmp) ;
+
+
+ _mm_store_pd(&C[16],Creg00) ;
+ _mm_store_pd(&C[18],Creg02) ;
+ _mm_store_pd(&C[20],Creg04) ;
+ _mm_store_pd(&C[24],Creg10) ;
+ _mm_store_pd(&C[26],Creg12) ;
+ _mm_store_pd(&C[28],Creg14) ;
+
+
+ /* Computing C(4:4,0:5) */
+
+ Areg0 = _mm_load_pd(&A[32]) ;
+
+ Breg0 = _mm_load_pd(&B[0]) ;
+ Breg2 = _mm_load_pd(&B[2]) ;
+ Breg4 = _mm_load_pd(&B[4]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+ Creg04 = Breg4 ;
+ Creg04 = _mm_mul_pd(Creg04,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[34]) ;
+
+ Breg0 = _mm_load_pd(&B[8]) ;
+ Breg2 = _mm_load_pd(&B[10]) ;
+ Breg4 = _mm_load_pd(&B[12]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[16]) ;
+ Breg2 = _mm_load_pd(&B[18]) ;
+ Breg4 = _mm_load_pd(&B[20]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[36]) ;
+
+ Breg0 = _mm_load_pd(&B[24]) ;
+ Breg2 = _mm_load_pd(&B[26]) ;
+ Breg4 = _mm_load_pd(&B[28]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[32]) ;
+ Breg2 = _mm_load_pd(&B[34]) ;
+ Breg4 = _mm_load_pd(&B[36]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+ Btmp = Breg4 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg04 = _mm_add_pd(Creg04,Btmp) ;
+
+
+ _mm_store_pd(&C[32],Creg00) ;
+ _mm_store_pd(&C[34],Creg02) ;
+ _mm_store_pd(&C[36],Creg04) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul3d_744.c.h b/src/USER-MGPT/mgpt_mmul3d_744.c.h
new file mode 100644
index 000000000..0f9043844
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul3d_744.c.h
@@ -0,0 +1,1116 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+void mmul3_7_8_4x4v2(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ __m128d
+ Creg00,Creg02,
+ Creg10,Creg12,
+ Creg20,Creg22,
+ Creg30,Creg32;
+ __m128d Areg0,Areg1,Areg2,Areg3;
+ __m128d Breg0,Breg2;
+ __m128d Atmp,Btmp;
+
+
+ /* Computing C(0:3,0:3) */
+
+ Areg0 = _mm_load_pd(&A[0]) ;
+ Areg1 = _mm_load_pd(&A[8]) ;
+ Areg2 = _mm_load_pd(&A[16]) ;
+ Areg3 = _mm_load_pd(&A[24]) ;
+
+ Breg0 = _mm_load_pd(&B[0]) ;
+ Breg2 = _mm_load_pd(&B[2]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_pd(Creg20,Atmp) ;
+ Creg22 = Breg2 ;
+ Creg22 = _mm_mul_pd(Creg22,Atmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Creg30 = Breg0 ;
+ Creg30 = _mm_mul_pd(Creg30,Atmp) ;
+ Creg32 = Breg2 ;
+ Creg32 = _mm_mul_pd(Creg32,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[2]) ;
+ Areg1 = _mm_load_pd(&A[10]) ;
+ Areg2 = _mm_load_pd(&A[18]) ;
+ Areg3 = _mm_load_pd(&A[26]) ;
+
+ Breg0 = _mm_load_pd(&B[8]) ;
+ Breg2 = _mm_load_pd(&B[10]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[16]) ;
+ Breg2 = _mm_load_pd(&B[18]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[4]) ;
+ Areg1 = _mm_load_pd(&A[12]) ;
+ Areg2 = _mm_load_pd(&A[20]) ;
+ Areg3 = _mm_load_pd(&A[28]) ;
+
+ Breg0 = _mm_load_pd(&B[24]) ;
+ Breg2 = _mm_load_pd(&B[26]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[32]) ;
+ Breg2 = _mm_load_pd(&B[34]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[6]) ;
+ Areg1 = _mm_load_pd(&A[14]) ;
+ Areg2 = _mm_load_pd(&A[22]) ;
+ Areg3 = _mm_load_pd(&A[30]) ;
+
+ Breg0 = _mm_load_pd(&B[40]) ;
+ Breg2 = _mm_load_pd(&B[42]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[48]) ;
+ Breg2 = _mm_load_pd(&B[50]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ _mm_store_pd(&C[0],Creg00) ;
+ _mm_store_pd(&C[2],Creg02) ;
+ _mm_store_pd(&C[8],Creg10) ;
+ _mm_store_pd(&C[10],Creg12) ;
+ _mm_store_pd(&C[16],Creg20) ;
+ _mm_store_pd(&C[18],Creg22) ;
+ _mm_store_pd(&C[24],Creg30) ;
+ _mm_store_pd(&C[26],Creg32) ;
+
+
+ /* Computing C(0:3,4:7) */
+
+ Areg0 = _mm_load_pd(&A[0]) ;
+ Areg1 = _mm_load_pd(&A[8]) ;
+ Areg2 = _mm_load_pd(&A[16]) ;
+ Areg3 = _mm_load_pd(&A[24]) ;
+
+ Breg0 = _mm_load_pd(&B[4]) ;
+ Breg2 = _mm_load_pd(&B[6]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_pd(Creg20,Atmp) ;
+ Creg22 = Breg2 ;
+ Creg22 = _mm_mul_pd(Creg22,Atmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Creg30 = Breg0 ;
+ Creg30 = _mm_mul_pd(Creg30,Atmp) ;
+ Creg32 = Breg2 ;
+ Creg32 = _mm_mul_pd(Creg32,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[2]) ;
+ Areg1 = _mm_load_pd(&A[10]) ;
+ Areg2 = _mm_load_pd(&A[18]) ;
+ Areg3 = _mm_load_pd(&A[26]) ;
+
+ Breg0 = _mm_load_pd(&B[12]) ;
+ Breg2 = _mm_load_pd(&B[14]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[20]) ;
+ Breg2 = _mm_load_pd(&B[22]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[4]) ;
+ Areg1 = _mm_load_pd(&A[12]) ;
+ Areg2 = _mm_load_pd(&A[20]) ;
+ Areg3 = _mm_load_pd(&A[28]) ;
+
+ Breg0 = _mm_load_pd(&B[28]) ;
+ Breg2 = _mm_load_pd(&B[30]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[36]) ;
+ Breg2 = _mm_load_pd(&B[38]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[6]) ;
+ Areg1 = _mm_load_pd(&A[14]) ;
+ Areg2 = _mm_load_pd(&A[22]) ;
+ Areg3 = _mm_load_pd(&A[30]) ;
+
+ Breg0 = _mm_load_pd(&B[44]) ;
+ Breg2 = _mm_load_pd(&B[46]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[52]) ;
+ Breg2 = _mm_load_pd(&B[54]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+ Atmp = Areg3 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg30 = _mm_add_pd(Creg30,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg32 = _mm_add_pd(Creg32,Btmp) ;
+
+
+ _mm_store_pd(&C[4],Creg00) ;
+ _mm_store_pd(&C[6],Creg02) ;
+ _mm_store_pd(&C[12],Creg10) ;
+ _mm_store_pd(&C[14],Creg12) ;
+ _mm_store_pd(&C[20],Creg20) ;
+ _mm_store_pd(&C[22],Creg22) ;
+ _mm_store_pd(&C[28],Creg30) ;
+ _mm_store_pd(&C[30],Creg32) ;
+
+
+ /* Computing C(4:6,0:3) */
+
+ Areg0 = _mm_load_pd(&A[32]) ;
+ Areg1 = _mm_load_pd(&A[40]) ;
+ Areg2 = _mm_load_pd(&A[48]) ;
+
+ Breg0 = _mm_load_pd(&B[0]) ;
+ Breg2 = _mm_load_pd(&B[2]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_pd(Creg20,Atmp) ;
+ Creg22 = Breg2 ;
+ Creg22 = _mm_mul_pd(Creg22,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[34]) ;
+ Areg1 = _mm_load_pd(&A[42]) ;
+ Areg2 = _mm_load_pd(&A[50]) ;
+
+ Breg0 = _mm_load_pd(&B[8]) ;
+ Breg2 = _mm_load_pd(&B[10]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[16]) ;
+ Breg2 = _mm_load_pd(&B[18]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[36]) ;
+ Areg1 = _mm_load_pd(&A[44]) ;
+ Areg2 = _mm_load_pd(&A[52]) ;
+
+ Breg0 = _mm_load_pd(&B[24]) ;
+ Breg2 = _mm_load_pd(&B[26]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[32]) ;
+ Breg2 = _mm_load_pd(&B[34]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[38]) ;
+ Areg1 = _mm_load_pd(&A[46]) ;
+ Areg2 = _mm_load_pd(&A[54]) ;
+
+ Breg0 = _mm_load_pd(&B[40]) ;
+ Breg2 = _mm_load_pd(&B[42]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[48]) ;
+ Breg2 = _mm_load_pd(&B[50]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ _mm_store_pd(&C[32],Creg00) ;
+ _mm_store_pd(&C[34],Creg02) ;
+ _mm_store_pd(&C[40],Creg10) ;
+ _mm_store_pd(&C[42],Creg12) ;
+ _mm_store_pd(&C[48],Creg20) ;
+ _mm_store_pd(&C[50],Creg22) ;
+
+
+ /* Computing C(4:6,4:7) */
+
+ Areg0 = _mm_load_pd(&A[32]) ;
+ Areg1 = _mm_load_pd(&A[40]) ;
+ Areg2 = _mm_load_pd(&A[48]) ;
+
+ Breg0 = _mm_load_pd(&B[4]) ;
+ Breg2 = _mm_load_pd(&B[6]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Creg00 = Breg0 ;
+ Creg00 = _mm_mul_pd(Creg00,Atmp) ;
+ Creg02 = Breg2 ;
+ Creg02 = _mm_mul_pd(Creg02,Atmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Creg10 = Breg0 ;
+ Creg10 = _mm_mul_pd(Creg10,Atmp) ;
+ Creg12 = Breg2 ;
+ Creg12 = _mm_mul_pd(Creg12,Atmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Creg20 = Breg0 ;
+ Creg20 = _mm_mul_pd(Creg20,Atmp) ;
+ Creg22 = Breg2 ;
+ Creg22 = _mm_mul_pd(Creg22,Atmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[34]) ;
+ Areg1 = _mm_load_pd(&A[42]) ;
+ Areg2 = _mm_load_pd(&A[50]) ;
+
+ Breg0 = _mm_load_pd(&B[12]) ;
+ Breg2 = _mm_load_pd(&B[14]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[20]) ;
+ Breg2 = _mm_load_pd(&B[22]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[36]) ;
+ Areg1 = _mm_load_pd(&A[44]) ;
+ Areg2 = _mm_load_pd(&A[52]) ;
+
+ Breg0 = _mm_load_pd(&B[28]) ;
+ Breg2 = _mm_load_pd(&B[30]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[36]) ;
+ Breg2 = _mm_load_pd(&B[38]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Areg0 = _mm_load_pd(&A[38]) ;
+ Areg1 = _mm_load_pd(&A[46]) ;
+ Areg2 = _mm_load_pd(&A[54]) ;
+
+ Breg0 = _mm_load_pd(&B[44]) ;
+ Breg2 = _mm_load_pd(&B[46]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ Breg0 = _mm_load_pd(&B[52]) ;
+ Breg2 = _mm_load_pd(&B[54]) ;
+
+ Atmp = Areg0 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg00 = _mm_add_pd(Creg00,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg02 = _mm_add_pd(Creg02,Btmp) ;
+
+ Atmp = Areg1 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg10 = _mm_add_pd(Creg10,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg12 = _mm_add_pd(Creg12,Btmp) ;
+
+ Atmp = Areg2 ;
+ Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ;
+ Btmp = Breg0 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg20 = _mm_add_pd(Creg20,Btmp) ;
+ Btmp = Breg2 ;
+ Btmp = _mm_mul_pd(Btmp,Atmp) ;
+ Creg22 = _mm_add_pd(Creg22,Btmp) ;
+
+
+ _mm_store_pd(&C[36],Creg00) ;
+ _mm_store_pd(&C[38],Creg02) ;
+ _mm_store_pd(&C[44],Creg10) ;
+ _mm_store_pd(&C[46],Creg12) ;
+ _mm_store_pd(&C[52],Creg20) ;
+ _mm_store_pd(&C[54],Creg22) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul_bg_552.c.h b/src/USER-MGPT/mgpt_mmul_bg_552.c.h
new file mode 100644
index 000000000..16c6e9e4a
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul_bg_552.c.h
@@ -0,0 +1,358 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+
+/* #define TESTING */
+
+#ifdef TESTING
+
+typedef struct {
+ double x,y;
+} pair;
+
+
+#define CPLX pair
+
+static double my_creal(CPLX x) {
+ return ((double *) &x)[0];
+}
+static double my_cimag(CPLX x) {
+ return ((double *) &x)[1];
+}
+static CPLX my_lfpd(const double *p) {
+ return ((CPLX *) p)[0];
+}
+static void my_stfpd(double *p,CPLX x) {
+ ((CPLX *) p)[0] = x;
+}
+static CPLX my_fxsmul(CPLX x,double a) {
+ double y[2];
+ y[0] = a * my_creal(x);
+ y[1] = a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) {
+ double y[2];
+ y[0] = my_creal(t) + a * my_creal(x);
+ y[1] = my_cimag(t) + a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+
+#define __creal my_creal
+#define __cimag my_cimag
+#define __lfpd my_lfpd
+#define __stfpd my_stfpd
+#define __fxsmul my_fxsmul
+#define __fxcpmadd my_fxcpmadd
+
+#else
+
+#define CPLX double _Complex
+
+#endif
+
+void mmul_bg_5_8_5x2v2(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ CPLX
+ Creg00,
+ Creg10,
+ Creg20,
+ Creg30,
+ Creg40;
+ CPLX Areg0,Areg1,Areg2,Areg3,Areg4;
+ CPLX Breg0;
+
+
+ /* Computing C(0:4,0:1) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+ Areg2 = __lfpd(&A[16]) ;
+ Areg3 = __lfpd(&A[24]) ;
+ Areg4 = __lfpd(&A[32]) ;
+
+ Breg0 = __lfpd(&B[0]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+ Areg2 = __lfpd(&A[18]) ;
+ Areg3 = __lfpd(&A[26]) ;
+ Areg4 = __lfpd(&A[34]) ;
+
+ Breg0 = __lfpd(&B[8]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[16]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+ Areg2 = __lfpd(&A[20]) ;
+ Areg3 = __lfpd(&A[28]) ;
+ Areg4 = __lfpd(&A[36]) ;
+
+ Breg0 = __lfpd(&B[24]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[32]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ __stfpd(&C[0],Creg00) ;
+ __stfpd(&C[8],Creg10) ;
+ __stfpd(&C[16],Creg20) ;
+ __stfpd(&C[24],Creg30) ;
+ __stfpd(&C[32],Creg40) ;
+
+
+ /* Computing C(0:4,2:3) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+ Areg2 = __lfpd(&A[16]) ;
+ Areg3 = __lfpd(&A[24]) ;
+ Areg4 = __lfpd(&A[32]) ;
+
+ Breg0 = __lfpd(&B[2]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+ Areg2 = __lfpd(&A[18]) ;
+ Areg3 = __lfpd(&A[26]) ;
+ Areg4 = __lfpd(&A[34]) ;
+
+ Breg0 = __lfpd(&B[10]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[18]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+ Areg2 = __lfpd(&A[20]) ;
+ Areg3 = __lfpd(&A[28]) ;
+ Areg4 = __lfpd(&A[36]) ;
+
+ Breg0 = __lfpd(&B[26]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[34]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ __stfpd(&C[2],Creg00) ;
+ __stfpd(&C[10],Creg10) ;
+ __stfpd(&C[18],Creg20) ;
+ __stfpd(&C[26],Creg30) ;
+ __stfpd(&C[34],Creg40) ;
+
+
+ /* Computing C(0:4,4:5) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+ Areg2 = __lfpd(&A[16]) ;
+ Areg3 = __lfpd(&A[24]) ;
+ Areg4 = __lfpd(&A[32]) ;
+
+ Breg0 = __lfpd(&B[4]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+ Areg2 = __lfpd(&A[18]) ;
+ Areg3 = __lfpd(&A[26]) ;
+ Areg4 = __lfpd(&A[34]) ;
+
+ Breg0 = __lfpd(&B[12]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[20]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+ Areg2 = __lfpd(&A[20]) ;
+ Areg3 = __lfpd(&A[28]) ;
+ Areg4 = __lfpd(&A[36]) ;
+
+ Breg0 = __lfpd(&B[28]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ;
+
+
+ Breg0 = __lfpd(&B[36]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+ Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ;
+
+ Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ;
+
+ Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ;
+
+
+ __stfpd(&C[4],Creg00) ;
+ __stfpd(&C[12],Creg10) ;
+ __stfpd(&C[20],Creg20) ;
+ __stfpd(&C[28],Creg30) ;
+ __stfpd(&C[36],Creg40) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul_bg_722.c.h b/src/USER-MGPT/mgpt_mmul_bg_722.c.h
new file mode 100644
index 000000000..e9821436e
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul_bg_722.c.h
@@ -0,0 +1,1075 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+
+/* #define TESTING */
+
+#ifdef TESTING
+
+typedef struct {
+ double x,y;
+} pair;
+
+
+#define CPLX pair
+
+static double my_creal(CPLX x) {
+ return ((double *) &x)[0];
+}
+static double my_cimag(CPLX x) {
+ return ((double *) &x)[1];
+}
+static CPLX my_lfpd(const double *p) {
+ return ((CPLX *) p)[0];
+}
+static void my_stfpd(double *p,CPLX x) {
+ ((CPLX *) p)[0] = x;
+}
+static CPLX my_fxsmul(CPLX x,double a) {
+ double y[2];
+ y[0] = a * my_creal(x);
+ y[1] = a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) {
+ double y[2];
+ y[0] = my_creal(t) + a * my_creal(x);
+ y[1] = my_cimag(t) + a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+
+#define __creal my_creal
+#define __cimag my_cimag
+#define __lfpd my_lfpd
+#define __stfpd my_stfpd
+#define __fxsmul my_fxsmul
+#define __fxcpmadd my_fxcpmadd
+
+#else
+
+#define CPLX double _Complex
+
+#endif
+
+void mmul_bg_7_8_2x2v2(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ CPLX
+ Creg00,
+ Creg10;
+ CPLX Areg0,Areg1;
+ CPLX Breg0;
+
+
+ /* Computing C(0:1,0:1) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+
+ Breg0 = __lfpd(&B[0]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+
+ Breg0 = __lfpd(&B[8]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[16]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+
+ Breg0 = __lfpd(&B[24]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[32]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[6]) ;
+ Areg1 = __lfpd(&A[14]) ;
+
+ Breg0 = __lfpd(&B[40]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[48]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[0],Creg00) ;
+ __stfpd(&C[8],Creg10) ;
+
+
+ /* Computing C(0:1,2:3) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+
+ Breg0 = __lfpd(&B[2]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+
+ Breg0 = __lfpd(&B[10]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[18]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+
+ Breg0 = __lfpd(&B[26]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[34]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[6]) ;
+ Areg1 = __lfpd(&A[14]) ;
+
+ Breg0 = __lfpd(&B[42]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[50]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[2],Creg00) ;
+ __stfpd(&C[10],Creg10) ;
+
+
+ /* Computing C(0:1,4:5) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+
+ Breg0 = __lfpd(&B[4]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+
+ Breg0 = __lfpd(&B[12]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[20]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+
+ Breg0 = __lfpd(&B[28]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[36]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[6]) ;
+ Areg1 = __lfpd(&A[14]) ;
+
+ Breg0 = __lfpd(&B[44]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[52]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[4],Creg00) ;
+ __stfpd(&C[12],Creg10) ;
+
+
+ /* Computing C(0:1,6:7) */
+
+ Areg0 = __lfpd(&A[0]) ;
+ Areg1 = __lfpd(&A[8]) ;
+
+ Breg0 = __lfpd(&B[6]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[2]) ;
+ Areg1 = __lfpd(&A[10]) ;
+
+ Breg0 = __lfpd(&B[14]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[22]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[4]) ;
+ Areg1 = __lfpd(&A[12]) ;
+
+ Breg0 = __lfpd(&B[30]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[38]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[6]) ;
+ Areg1 = __lfpd(&A[14]) ;
+
+ Breg0 = __lfpd(&B[46]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[54]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[6],Creg00) ;
+ __stfpd(&C[14],Creg10) ;
+
+
+ /* Computing C(2:3,0:1) */
+
+ Areg0 = __lfpd(&A[16]) ;
+ Areg1 = __lfpd(&A[24]) ;
+
+ Breg0 = __lfpd(&B[0]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[18]) ;
+ Areg1 = __lfpd(&A[26]) ;
+
+ Breg0 = __lfpd(&B[8]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[16]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[20]) ;
+ Areg1 = __lfpd(&A[28]) ;
+
+ Breg0 = __lfpd(&B[24]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[32]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[22]) ;
+ Areg1 = __lfpd(&A[30]) ;
+
+ Breg0 = __lfpd(&B[40]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[48]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[16],Creg00) ;
+ __stfpd(&C[24],Creg10) ;
+
+
+ /* Computing C(2:3,2:3) */
+
+ Areg0 = __lfpd(&A[16]) ;
+ Areg1 = __lfpd(&A[24]) ;
+
+ Breg0 = __lfpd(&B[2]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[18]) ;
+ Areg1 = __lfpd(&A[26]) ;
+
+ Breg0 = __lfpd(&B[10]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[18]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[20]) ;
+ Areg1 = __lfpd(&A[28]) ;
+
+ Breg0 = __lfpd(&B[26]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[34]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[22]) ;
+ Areg1 = __lfpd(&A[30]) ;
+
+ Breg0 = __lfpd(&B[42]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[50]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[18],Creg00) ;
+ __stfpd(&C[26],Creg10) ;
+
+
+ /* Computing C(2:3,4:5) */
+
+ Areg0 = __lfpd(&A[16]) ;
+ Areg1 = __lfpd(&A[24]) ;
+
+ Breg0 = __lfpd(&B[4]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[18]) ;
+ Areg1 = __lfpd(&A[26]) ;
+
+ Breg0 = __lfpd(&B[12]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[20]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[20]) ;
+ Areg1 = __lfpd(&A[28]) ;
+
+ Breg0 = __lfpd(&B[28]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[36]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[22]) ;
+ Areg1 = __lfpd(&A[30]) ;
+
+ Breg0 = __lfpd(&B[44]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[52]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[20],Creg00) ;
+ __stfpd(&C[28],Creg10) ;
+
+
+ /* Computing C(2:3,6:7) */
+
+ Areg0 = __lfpd(&A[16]) ;
+ Areg1 = __lfpd(&A[24]) ;
+
+ Breg0 = __lfpd(&B[6]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[18]) ;
+ Areg1 = __lfpd(&A[26]) ;
+
+ Breg0 = __lfpd(&B[14]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[22]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[20]) ;
+ Areg1 = __lfpd(&A[28]) ;
+
+ Breg0 = __lfpd(&B[30]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[38]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[22]) ;
+ Areg1 = __lfpd(&A[30]) ;
+
+ Breg0 = __lfpd(&B[46]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[54]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[22],Creg00) ;
+ __stfpd(&C[30],Creg10) ;
+
+
+ /* Computing C(4:5,0:1) */
+
+ Areg0 = __lfpd(&A[32]) ;
+ Areg1 = __lfpd(&A[40]) ;
+
+ Breg0 = __lfpd(&B[0]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[34]) ;
+ Areg1 = __lfpd(&A[42]) ;
+
+ Breg0 = __lfpd(&B[8]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[16]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[36]) ;
+ Areg1 = __lfpd(&A[44]) ;
+
+ Breg0 = __lfpd(&B[24]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[32]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[38]) ;
+ Areg1 = __lfpd(&A[46]) ;
+
+ Breg0 = __lfpd(&B[40]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[48]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[32],Creg00) ;
+ __stfpd(&C[40],Creg10) ;
+
+
+ /* Computing C(4:5,2:3) */
+
+ Areg0 = __lfpd(&A[32]) ;
+ Areg1 = __lfpd(&A[40]) ;
+
+ Breg0 = __lfpd(&B[2]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[34]) ;
+ Areg1 = __lfpd(&A[42]) ;
+
+ Breg0 = __lfpd(&B[10]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[18]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[36]) ;
+ Areg1 = __lfpd(&A[44]) ;
+
+ Breg0 = __lfpd(&B[26]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[34]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[38]) ;
+ Areg1 = __lfpd(&A[46]) ;
+
+ Breg0 = __lfpd(&B[42]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[50]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[34],Creg00) ;
+ __stfpd(&C[42],Creg10) ;
+
+
+ /* Computing C(4:5,4:5) */
+
+ Areg0 = __lfpd(&A[32]) ;
+ Areg1 = __lfpd(&A[40]) ;
+
+ Breg0 = __lfpd(&B[4]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[34]) ;
+ Areg1 = __lfpd(&A[42]) ;
+
+ Breg0 = __lfpd(&B[12]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[20]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[36]) ;
+ Areg1 = __lfpd(&A[44]) ;
+
+ Breg0 = __lfpd(&B[28]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[36]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[38]) ;
+ Areg1 = __lfpd(&A[46]) ;
+
+ Breg0 = __lfpd(&B[44]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[52]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[36],Creg00) ;
+ __stfpd(&C[44],Creg10) ;
+
+
+ /* Computing C(4:5,6:7) */
+
+ Areg0 = __lfpd(&A[32]) ;
+ Areg1 = __lfpd(&A[40]) ;
+
+ Breg0 = __lfpd(&B[6]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[34]) ;
+ Areg1 = __lfpd(&A[42]) ;
+
+ Breg0 = __lfpd(&B[14]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[22]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[36]) ;
+ Areg1 = __lfpd(&A[44]) ;
+
+ Breg0 = __lfpd(&B[30]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[38]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ Areg0 = __lfpd(&A[38]) ;
+ Areg1 = __lfpd(&A[46]) ;
+
+ Breg0 = __lfpd(&B[46]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ;
+
+
+ Breg0 = __lfpd(&B[54]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+ Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ;
+
+
+ __stfpd(&C[38],Creg00) ;
+ __stfpd(&C[46],Creg10) ;
+
+
+ /* Computing C(6:6,0:1) */
+
+ Areg0 = __lfpd(&A[48]) ;
+
+ Breg0 = __lfpd(&B[0]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[50]) ;
+
+ Breg0 = __lfpd(&B[8]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[16]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[52]) ;
+
+ Breg0 = __lfpd(&B[24]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[32]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[54]) ;
+
+ Breg0 = __lfpd(&B[40]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[48]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ __stfpd(&C[48],Creg00) ;
+
+
+ /* Computing C(6:6,2:3) */
+
+ Areg0 = __lfpd(&A[48]) ;
+
+ Breg0 = __lfpd(&B[2]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[50]) ;
+
+ Breg0 = __lfpd(&B[10]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[18]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[52]) ;
+
+ Breg0 = __lfpd(&B[26]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[34]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[54]) ;
+
+ Breg0 = __lfpd(&B[42]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[50]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ __stfpd(&C[50],Creg00) ;
+
+
+ /* Computing C(6:6,4:5) */
+
+ Areg0 = __lfpd(&A[48]) ;
+
+ Breg0 = __lfpd(&B[4]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[50]) ;
+
+ Breg0 = __lfpd(&B[12]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[20]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[52]) ;
+
+ Breg0 = __lfpd(&B[28]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[36]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[54]) ;
+
+ Breg0 = __lfpd(&B[44]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[52]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ __stfpd(&C[52],Creg00) ;
+
+
+ /* Computing C(6:6,6:7) */
+
+ Areg0 = __lfpd(&A[48]) ;
+
+ Breg0 = __lfpd(&B[6]) ;
+
+ Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[50]) ;
+
+ Breg0 = __lfpd(&B[14]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[22]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[52]) ;
+
+ Breg0 = __lfpd(&B[30]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[38]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ Areg0 = __lfpd(&A[54]) ;
+
+ Breg0 = __lfpd(&B[46]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ;
+
+
+ Breg0 = __lfpd(&B[54]) ;
+
+ Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ;
+
+
+ __stfpd(&C[54],Creg00) ;
+
+
+}
diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h
new file mode 100644
index 000000000..2e38b5b0c
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h
@@ -0,0 +1,236 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#define vector vector4double
+#define const
+#define vec_fma vec_madd
+
+void mmul_bgq_n5_lda8_2x8(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ vector
+ Creg00,Creg04,
+ Creg10,Creg14;
+ vector Areg0,Areg1;
+ vector Breg0,Breg4;
+ vector Atmp;
+
+
+ /* Computing C(0:1,0:5) */
+
+ Areg0 = vec_ld(8*0,A) ;
+ Areg1 = vec_ld(8*8,A) ;
+
+ Breg0 = vec_ld(8*0,B) ;
+ Breg4 = vec_ld(8*4,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_mul(Atmp,Breg0) ;
+ Creg04 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_mul(Atmp,Breg0) ;
+ Creg14 = vec_mul(Atmp,Breg4) ;
+
+
+ Breg0 = vec_ld(8*8,B) ;
+ Breg4 = vec_ld(8*12,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Breg0 = vec_ld(8*16,B) ;
+ Breg4 = vec_ld(8*20,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Areg0 = vec_ld(8*4,A) ;
+ Areg1 = vec_ld(8*12,A) ;
+
+ Breg0 = vec_ld(8*24,B) ;
+ Breg4 = vec_ld(8*28,B) ;
+
+ Atmp = vec_splat(Areg0,0) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,0) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Breg0 = vec_ld(8*32,B) ;
+ Breg4 = vec_ld(8*36,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ vec_st(Creg00,8*0,C) ;
+ vec_st(Creg04,8*4,C) ;
+ vec_st(Creg10,8*8,C) ;
+ vec_st(Creg14,8*12,C) ;
+
+
+ /* Computing C(2:3,0:5) */
+
+ Areg0 = vec_ld(8*16,A) ;
+ Areg1 = vec_ld(8*24,A) ;
+
+ Breg0 = vec_ld(8*0,B) ;
+ Breg4 = vec_ld(8*4,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_mul(Atmp,Breg0) ;
+ Creg04 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_mul(Atmp,Breg0) ;
+ Creg14 = vec_mul(Atmp,Breg4) ;
+
+
+ Breg0 = vec_ld(8*8,B) ;
+ Breg4 = vec_ld(8*12,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Breg0 = vec_ld(8*16,B) ;
+ Breg4 = vec_ld(8*20,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Areg0 = vec_ld(8*20,A) ;
+ Areg1 = vec_ld(8*28,A) ;
+
+ Breg0 = vec_ld(8*24,B) ;
+ Breg4 = vec_ld(8*28,B) ;
+
+ Atmp = vec_splat(Areg0,0) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,0) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ Breg0 = vec_ld(8*32,B) ;
+ Breg4 = vec_ld(8*36,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+
+ vec_st(Creg00,8*16,C) ;
+ vec_st(Creg04,8*20,C) ;
+ vec_st(Creg10,8*24,C) ;
+ vec_st(Creg14,8*28,C) ;
+
+
+ /* Computing C(4:4,0:5) */
+
+ Areg0 = vec_ld(8*32,A) ;
+
+ Breg0 = vec_ld(8*0,B) ;
+ Breg4 = vec_ld(8*4,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_mul(Atmp,Breg0) ;
+ Creg04 = vec_mul(Atmp,Breg4) ;
+
+
+ Breg0 = vec_ld(8*8,B) ;
+ Breg4 = vec_ld(8*12,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+
+ Breg0 = vec_ld(8*16,B) ;
+ Breg4 = vec_ld(8*20,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+
+ Areg0 = vec_ld(8*36,A) ;
+
+ Breg0 = vec_ld(8*24,B) ;
+ Breg4 = vec_ld(8*28,B) ;
+
+ Atmp = vec_splat(Areg0,0) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+
+ Breg0 = vec_ld(8*32,B) ;
+ Breg4 = vec_ld(8*36,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+
+ vec_st(Creg00,8*32,C) ;
+ vec_st(Creg04,8*36,C) ;
+
+
+}
+
+#undef vector
+#undef const
+#undef vec_fma
diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h
new file mode 100644
index 000000000..26f36c484
--- /dev/null
+++ b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h
@@ -0,0 +1,332 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#define vector vector4double
+#define const
+#define vec_fma vec_madd
+
+void mmul_bgq_n7_lda8_4x8(const double * restrict A,
+ const double * restrict B,
+ double * restrict C) {
+ vector
+ Creg00,Creg04,
+ Creg10,Creg14,
+ Creg20,Creg24,
+ Creg30,Creg34;
+ vector Areg0,Areg1,Areg2,Areg3;
+ vector Breg0,Breg4;
+ vector Atmp;
+
+
+ /* Computing C(0:3,0:7) */
+
+ Areg0 = vec_ld(8*0,A) ;
+ Areg1 = vec_ld(8*8,A) ;
+ Areg2 = vec_ld(8*16,A) ;
+ Areg3 = vec_ld(8*24,A) ;
+
+ Breg0 = vec_ld(8*0,B) ;
+ Breg4 = vec_ld(8*4,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_mul(Atmp,Breg0) ;
+ Creg04 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_mul(Atmp,Breg0) ;
+ Creg14 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg2,1) ;
+ Creg20 = vec_mul(Atmp,Breg0) ;
+ Creg24 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg3,1) ;
+ Creg30 = vec_mul(Atmp,Breg0) ;
+ Creg34 = vec_mul(Atmp,Breg4) ;
+
+
+ Breg0 = vec_ld(8*8,B) ;
+ Breg4 = vec_ld(8*12,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,2) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,2) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ Breg0 = vec_ld(8*16,B) ;
+ Breg4 = vec_ld(8*20,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,3) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,3) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ Areg0 = vec_ld(8*4,A) ;
+ Areg1 = vec_ld(8*12,A) ;
+ Areg2 = vec_ld(8*20,A) ;
+ Areg3 = vec_ld(8*28,A) ;
+
+ Breg0 = vec_ld(8*24,B) ;
+ Breg4 = vec_ld(8*28,B) ;
+
+ Atmp = vec_splat(Areg0,0) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,0) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,0) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,0) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ Breg0 = vec_ld(8*32,B) ;
+ Breg4 = vec_ld(8*36,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,1) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,1) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ Breg0 = vec_ld(8*40,B) ;
+ Breg4 = vec_ld(8*44,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,2) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,2) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ Breg0 = vec_ld(8*48,B) ;
+ Breg4 = vec_ld(8*52,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,3) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+ Atmp = vec_splat(Areg3,3) ;
+ Creg30 = vec_fma(Atmp,Breg0,Creg30) ;
+ Creg34 = vec_fma(Atmp,Breg4,Creg34) ;
+
+
+ vec_st(Creg00,8*0,C) ;
+ vec_st(Creg04,8*4,C) ;
+ vec_st(Creg10,8*8,C) ;
+ vec_st(Creg14,8*12,C) ;
+ vec_st(Creg20,8*16,C) ;
+ vec_st(Creg24,8*20,C) ;
+ vec_st(Creg30,8*24,C) ;
+ vec_st(Creg34,8*28,C) ;
+
+
+ /* Computing C(4:6,0:7) */
+
+ Areg0 = vec_ld(8*32,A) ;
+ Areg1 = vec_ld(8*40,A) ;
+ Areg2 = vec_ld(8*48,A) ;
+
+ Breg0 = vec_ld(8*0,B) ;
+ Breg4 = vec_ld(8*4,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_mul(Atmp,Breg0) ;
+ Creg04 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_mul(Atmp,Breg0) ;
+ Creg14 = vec_mul(Atmp,Breg4) ;
+
+ Atmp = vec_splat(Areg2,1) ;
+ Creg20 = vec_mul(Atmp,Breg0) ;
+ Creg24 = vec_mul(Atmp,Breg4) ;
+
+
+ Breg0 = vec_ld(8*8,B) ;
+ Breg4 = vec_ld(8*12,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,2) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ Breg0 = vec_ld(8*16,B) ;
+ Breg4 = vec_ld(8*20,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,3) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ Areg0 = vec_ld(8*36,A) ;
+ Areg1 = vec_ld(8*44,A) ;
+ Areg2 = vec_ld(8*52,A) ;
+
+ Breg0 = vec_ld(8*24,B) ;
+ Breg4 = vec_ld(8*28,B) ;
+
+ Atmp = vec_splat(Areg0,0) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,0) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,0) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ Breg0 = vec_ld(8*32,B) ;
+ Breg4 = vec_ld(8*36,B) ;
+
+ Atmp = vec_splat(Areg0,1) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,1) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,1) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ Breg0 = vec_ld(8*40,B) ;
+ Breg4 = vec_ld(8*44,B) ;
+
+ Atmp = vec_splat(Areg0,2) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,2) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,2) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ Breg0 = vec_ld(8*48,B) ;
+ Breg4 = vec_ld(8*52,B) ;
+
+ Atmp = vec_splat(Areg0,3) ;
+ Creg00 = vec_fma(Atmp,Breg0,Creg00) ;
+ Creg04 = vec_fma(Atmp,Breg4,Creg04) ;
+
+ Atmp = vec_splat(Areg1,3) ;
+ Creg10 = vec_fma(Atmp,Breg0,Creg10) ;
+ Creg14 = vec_fma(Atmp,Breg4,Creg14) ;
+
+ Atmp = vec_splat(Areg2,3) ;
+ Creg20 = vec_fma(Atmp,Breg0,Creg20) ;
+ Creg24 = vec_fma(Atmp,Breg4,Creg24) ;
+
+
+ vec_st(Creg00,8*32,C) ;
+ vec_st(Creg04,8*36,C) ;
+ vec_st(Creg10,8*40,C) ;
+ vec_st(Creg14,8*44,C) ;
+ vec_st(Creg20,8*48,C) ;
+ vec_st(Creg24,8*52,C) ;
+
+
+}
+
+#undef vector
+#undef const
+#undef vec_fma
diff --git a/src/USER-MGPT/mgpt_readpot.cpp b/src/USER-MGPT/mgpt_readpot.cpp
new file mode 100644
index 000000000..bfbb15ddc
--- /dev/null
+++ b/src/USER-MGPT/mgpt_readpot.cpp
@@ -0,0 +1,566 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include "mgpt_splinetab.h"
+
+#include "mgpt_readpot.h"
+
+static double fgauss(double x,double al) {
+ return exp(-al * pow(x-1.0, 2));
+}
+static double hgauss(double x,double al) {
+ return (1.0 + al * pow(x-1.0, 2)) * exp(-al * pow(x-1.0, 2));
+}
+static double fl(double r,int mode,double rp,double p1,double al,double r0,double pn)
+{
+ double term;
+ //double pn=1.0;
+ if (mode <= 4)
+ term = pow(rp/r, p1);
+ else
+ term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn);
+
+ if (r <= r0) return term;
+ double quan = al*(r/r0 - 1.0)*(r/r0 - 1.0);
+ if(mode <= 2)
+ return term*exp(-quan);
+ else
+ return term*(1.0 + quan)*exp(-quan);
+}
+
+static int cmp_double(const void *ap,const void *bp) {
+ double a = *((const double *) ap);
+ double b = *((const double *) bp);
+ if(a < b)
+ return -1;
+ else if(a > b)
+ return 1;
+ else
+ return 0;
+}
+static void getparmindata(const char *potin_file,int nvol[1],double vol0[1],double x0[1],double x1[1]) {
+ int n,vsize;
+ double *volarr;
+ char metal[80],metalx[80];
+ int ipot,ipotx,mode,modex;
+ FILE *in = fopen(potin_file,"r");
+ char line[1024];
+
+ if(in == NULL) {
+ fprintf(stderr,"@%s:%d: Error reading potin file. Can not open file \'%s\'.\n",
+ __FILE__,__LINE__,potin_file);
+ exit(1);
+ }
+
+ vsize = 10;
+ volarr = (double *) malloc(sizeof(double) * vsize);
+ n = 0;
+ while(fgets(line,sizeof(line),in) != NULL) {
+ double zval,ivol,rws,mass;
+ double r0x,r1x,drx;
+ int nrx,i;
+
+ if(line[strspn(line," \t")] == '#') continue;
+
+ if(n == 0) {
+ metal[0] = 0;
+ if(sscanf(line,"%s %d %d",metal,&ipot,&mode) != 3) {
+ fprintf(stderr,"@%s:%d: Error on potin file. line = %s\n",
+ __FILE__,__LINE__,line);
+ exit(1);
+ }
+ } else {
+ metalx[0] = 0;
+ if(sscanf(line,"%s %d %d",metalx,&ipotx,&modex) != 3) {
+ fprintf(stderr,"@%s:%d: Error on potin file. line = %s\n",
+ __FILE__,__LINE__,line);
+ exit(1);
+ } else if(strcmp(metal,metalx) != 0 || ipot != ipotx || mode != modex) {
+ fprintf(stderr,"@%s:%d: Error on potin file, parameter mismatch:\n"
+ " metal = \'%s\' ipot = %d mode = %d\n"
+ " metalx = \'%s\' ipotx = %d modex = %d\n",
+ __FILE__,__LINE__,
+ metal,ipot,mode,
+ metalx,ipotx,modex);
+ exit(1);
+ }
+ }
+
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf",&zval,&ivol,&rws,&mass);
+ if(n >= vsize) {
+ vsize = 2*vsize;
+ volarr = (double *) realloc(volarr,sizeof(double) * vsize);
+ }
+ volarr[n] = ivol;
+ n = n + 1;
+
+ for(i = 0; i<5; i++)
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf",&r0x,&r1x,&drx);
+ nrx = (int) ((r1x-r0x)/drx + 1.1); /* Really: 1+round((r1-r0)/dr) */
+ for(i = 0; i<nrx; i++)
+ fgets(line,sizeof(line),in);
+ }
+ fclose(in);
+
+ if(n == 0) {
+ fprintf(stderr,"@%s:%d: Invalid potin file \'%s\', no volume records.\n",
+ __FILE__,__LINE__,potin_file);
+ exit(1);
+ }
+
+ if(0) {
+ printf("Before sort:\n");
+ for(int i = 0; i<n; i++)
+ printf("%3d :: %.3f%s",i,volarr[i], (i%5==4) ? "\n" : " ");
+ printf("\n\n");
+ }
+ qsort(volarr,n,sizeof(double),cmp_double);
+
+ if(0) {
+ printf("After sort:\n");
+ for(int i = 0; i<n; i++)
+ printf("%3d :: %.3f%s",i,volarr[i], (i%5==4) ? "\n" : " ");
+ printf("\n\n");
+ }
+
+ nvol[0] = n;
+ vol0[0] = volarr[n/2];
+ x0[0] = pow(volarr[0]/vol0[0],1.0/3.0);
+ x1[0] = pow(volarr[n-1]/vol0[0],1.0/3.0);
+
+ free(volarr);
+}
+
+void potdata::readpot(const char *parmin_file,const char *potin_file,const double vol) {
+ FILE *in;
+ double x0,x1,dx,dr;
+ int nx;
+
+ double r0x,r1x,drx;
+ int nrx;
+
+ char metalx[80];
+ int ipotx,modex; double pnx;
+ double vol0;
+
+ double *vatab,*vbtab,*vctab,*vdtab,*vetab,*p1tab,*altab,*vpairtab = 0;
+ double *r0rwstab,*evol0tab;
+ double (*C)[4];
+ double *y,*dy;
+ double x,dxdv;
+ double unused;
+
+ double zval,rws,ivol,r0rws,rcrws,rmrws;//,mass
+
+ int i,j;
+ int L;
+
+ char line[1024];
+
+ input_vol = vol;
+
+ /* Read potential data */
+ in = fopen(parmin_file,"r");
+ do {
+ fgets(line,sizeof(line),in);
+ } while(line[strspn(line," \t")] == '#');
+
+ /* Test to see whether this is a one-line or two-line version of parmin */
+ if(sscanf(line,"%lf %lf %lf %lf %d",&ddl[1],&ddl[2],&ddl[3],&ddl[4],&L) == 5) {
+ /* One-line version, call getparmindata to figure out volume table spacing. */
+ int nvol;
+ getparmindata(potin_file,&nvol,&vol0,&x0,&x1);
+ dx = (x1-x0)/(nvol-1);
+ if(0) {
+ printf("getparmindata() ==> nvol = %d, vol0 = %.6f, x0= %.6f, x1 = %.6f, dx = %.6f\n",
+ nvol,vol0,x0,x1,dx);
+ }
+ } else {
+ /* Two-line version, reparse this line, and read second line */
+ sscanf(line,"%lf %lf %lf %lf",&x0,&x1,&dx,&vol0);
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf %d",&ddl[1],&ddl[2],&ddl[3],&ddl[4],&L);
+
+ }
+ double rws_scale = pow(3.0*vol0/(16.0*atan(1.0)),1.0/3.0);
+ fclose(in);
+
+ lang = L+1;
+ lmax = 2*L+1;
+ double s = ddl[1],p = ddl[2],d = ddl[3],f = ddl[4];
+ double ss = s*s, pp = p*p, dd = d*d, ff = f*f;
+ anorm3 = s*ss + 2.0*( p*pp + d*dd + f*ff);
+ anorm4 = ss*ss + 2.0*(pp*pp + dd*dd + ff*ff);
+ /*
+ for(i = 1; i<=lmax; i++) {
+ for(j = 1; j<=lmax; j++)
+ del0.m[i][j] = 0.0;
+ del0[i][i] = 1.0;
+ }
+ Matrix::sz = lmax;
+ */
+ nx = (int) ((x1-x0)/dx + 1.1); /* Really: 1+round((x1-x0)/dx) */
+ vatab = new double[nx];
+ vbtab = new double[nx];
+ vctab = new double[nx];
+ vdtab = new double[nx];
+ vetab = new double[nx];
+
+ p1tab = new double[nx];
+ altab = new double[nx];
+
+ r0rwstab = new double[nx];
+ evol0tab = new double[nx];
+
+ in = fopen(potin_file,"r");
+
+ int *tag = new int[nx];
+ for(i = 0; i<nx; i++) tag[i] = 0;
+
+ int ii;
+ for(ii = 0; ii<nx; ii++) {
+
+ do {
+ fgets(line,sizeof(line),in);
+ } while(line[strspn(line," \t")] == '#');
+
+ metalx[0] = 0;
+
+ /* Read element type, mode, and pn parameter */ {
+ int nf = sscanf(line,"%s %d %d %lf",metalx,&ipotx,&modex,&pnx);
+ if(nf < 3) {
+ printf("Error in %s() @ %s:%d: Inconsistency in potential input file (%s) "
+ "at record %d:\n"
+ " Expected at least three fields. Number of fields = %d\n",
+ __func__,__FILE__,__LINE__,potin_file,ii,
+ nf);
+ exit(1);
+ }
+ if(modex <= 4) {
+ pnx = 1.0;
+ } else if(modex <= 6) {
+ if(nf != 4) {
+ printf("Error in %s() @ %s:%d: Inconsistency in potential input file (%s) "
+ "at record %d:\n"
+ " mode = %d, number of fields = %d\n",
+ __func__,__FILE__,__LINE__,potin_file,ii,
+ modex,nf);
+ exit(1);
+ }
+ } else {
+ printf("Error in %s() @ %s:%d: Inconsistency in potential input file (%s): "
+ "at record %d\n"
+ " Invalid mode. mode = %d\n",
+ __func__,__FILE__,__LINE__,potin_file,ii,
+ modex);
+ }
+ }
+
+ if(ii == 0) {
+ sscanf(line,"%s %d %d %lf",metal,&ipot,&mode,&pn);
+ if(modex <= 4) pn = pnx;
+ } else {
+ /* Check that {metal,ipot,mode}x == {metal,ipot,mode} */
+ if(strcmp(metal,metalx) != 0 ||
+ ipotx != ipot ||
+ modex != mode ||
+ pnx != pn) {
+ printf("Error in %s() @ %s:%d: Inconsistency in potential input file (%s) "
+ "at record %d:\n"
+ "metalx != metal (%s != %s) or\n"
+ "ipotx != ipot (%d != %d) or\n"
+ "modex != mode (%d != %d) or\n"
+ "pnx != pn (%.3f != %.3f).\n",
+ __func__,__FILE__,__LINE__,potin_file,ii,
+ metalx,metal,
+ ipotx,ipot,
+ modex,mode,
+ pnx,pn);
+ exit(1);
+ }
+ }
+ //printf("LINE: %s\n",line);
+ //printf("metal = \'%s\' ipot = %d mode = %d\n",metalx,ipotx,modex);
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf",&zval,&ivol,&rws,&mass);
+ /*{
+ double xi = x0 + i/((double) (nx-1)) * (x1-x0);
+ double volguess = vol0 * xi*xi*xi;
+ if(fabs(volguess/ivol - 1.0) > 1e-3)
+ printf("Wrong volume guess, i=%d volgues=%15.5e ivol=%15.5e\n",
+ i,volguess,ivol);
+ }*/
+
+ double ifrac = (pow(ivol/vol0,1.0/3.0) - x0)/((x1-x0)/(nx-1));
+ i = (int) (ifrac + 0.1);
+ if(fabs(i - ifrac) > 0.01) {
+ printf("Volume point not in table... ii=%d i=%d ifrac=%15.5e vol=%15.5e\n",
+ ii,i,ifrac,ivol);
+ printf("vol0 = %15.5e zval = %15.5e mass = %15.5e\n",vol0,zval,mass);
+ exit(1);
+ } else if(tag[i] == 1) {
+ printf("Duplicate volume point in table.... ii=%d i=%d ifrac=%15.5e vol=%15.5e\n",
+ ii,i,ifrac,ivol);
+ exit(1);
+ } else tag[i] = 1;
+
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf",&r0rwstab[i],&altab[i],&rcrws,&rmrws);
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf",&p1tab[i],&unused,&evol0tab[i]);
+
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf %lf",
+ &vatab[i],&vbtab[i],&vctab[i],&vdtab[i],&vetab[i]);
+ if(ipot == 1) {
+ vatab[i] *= vdtab[i];
+ vctab[i] *= vctab[i];
+ vetab[i] *= vetab[i];
+ }
+
+ fgets(line,sizeof(line),in);
+
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf",&r0x,&r1x,&drx);
+ nrx = (int) ((r1x-r0x)/drx + 1.1); /* Really: 1+round((r1-r0)/dr) */
+
+ if(ii == 0) {
+ r0 = r0x; r1 = r1x; dr = drx; nr = nrx;
+ vpairtab = new double[nx*nr];
+ } else {
+ /* Check that {r0,r1,dr,nr}x == {r0,r1,dr,nr} */
+ }
+
+ for(j = 0; j<nr; j++) {
+ double rj,ktan,dvdvol;
+ fgets(line,sizeof(line),in);
+ sscanf(line,"%lf %lf %lf %lf",
+ &rj,&vpairtab[i*nr+j],&ktan,&dvdvol);
+
+ { /* Add screening and fl() part to pair energy table */
+
+ double al = altab[i];
+ double p1 = p1tab[i];
+
+ int bscreen = (al > 0.0);
+
+ double xi = x0 + i/((double) (nx-1)) * (x1-x0);
+ double rws = rws_scale * xi;
+
+ double r0rws = r0rwstab[i];
+ double r00 = r0rws*rws,rp = 1.8*rws;
+ if(bscreen == 0) r0rws = 10.0;
+ double alp = al,alm = al;
+ if(mode == 2 || mode == 4 || mode == 6) alm = 125.0;
+ al = alp;
+
+ double r = r0 + j*(r1-r0)/(nr-1);
+
+ double rrws = r/rws;
+ //double rsqr = r*r;
+ // double fl(double r,int mode,double rp,double p1,double al,double r0)
+ double flr = fl(r,mode,rp,p1,al,r00,pn);
+ double fl2 = flr*flr;
+ double v2a = vatab[i]*fl2*fl2;
+ double v2b = vbtab[i]*fl2;
+ double fscr = 1.0;
+
+ if(bscreen == 1 && rrws >= r0rws) {
+ double arg = rrws/r0rwstab[i];
+ double arg1 = arg - 1.0;
+ double arg12 = arg1*arg1;
+ double f,dp;
+ if(mode <= 2) {
+ f = fgauss(arg,al);
+ dp=2.*al*arg*arg1;
+ }
+ else {
+ f = hgauss(arg,al);
+ double arg13 = arg1*arg12;
+ dp=2.0*al*al*arg*arg13/(1.+al*arg12);
+ }
+ fscr = f*f;
+ }
+
+ double vpair_tmp = vpairtab[i*nr+j];
+ vpairtab[i*nr+j] = vpairtab[i*nr+j]*fscr + v2a - v2b;
+
+ if(0) if(fabs(vol-ivol) < 0.01) {
+ static FILE *xfile = NULL;
+ if(j == 0) {
+ xfile = fopen("mgpt5-pot.dat","w");
+ fprintf(xfile,"%%%% vol = %15.5e ivol = %15.5e i = %d ii = %d\n",
+ vol,ivol,i,ii);
+ }
+ fprintf(xfile,"%15.5e %15.5e %15.5e %15.5e %15.5e %20.10e\n",
+ r,vpair_tmp,fscr,v2a,v2b,flr);
+ if(j == nr-1) fclose(xfile);
+ }
+
+
+ }
+
+ }
+ }
+ fclose(in);
+
+ for(i = 0; i<nx; i++)
+ if(tag[i] == 0) {
+ printf("Volume point missing in table. i = %d\n",i);
+ exit(1);
+ }
+
+ /* Make table */
+ x = pow(vol/vol0,1.0/3.0);
+ dxdv = 1.0/(3.0*vol0*x*x);
+
+ C = new double[(nr > nx) ? nr : nx][4];
+ makespline(nx,1,vatab,C);
+ evalspline(nx-1,x0,x1,C,x,&va,&dva,&unused);
+ dva *= dxdv;
+
+ makespline(nx,1,vbtab,C);
+ evalspline(nx-1,x0,x1,C,x,&vb,&dvb,&unused);
+ dvb *= dxdv;
+
+ makespline(nx,1,vctab,C);
+ evalspline(nx-1,x0,x1,C,x,&vc,&dvc,&unused);
+ dvc *= dxdv;
+
+ makespline(nx,1,vdtab,C);
+ evalspline(nx-1,x0,x1,C,x,&vd,&dvd,&unused);
+ dvd *= dxdv;
+
+ makespline(nx,1,vetab,C);
+ evalspline(nx-1,x0,x1,C,x,&ve,&dve,&unused);
+ dve *= dxdv;
+
+ makespline(nx,1,p1tab,C);
+ evalspline(nx-1,x0,x1,C,x,&p1,&dp1,&unused);
+ dp1 *= dxdv;
+
+ makespline(nx,1,altab,C);
+ evalspline(nx-1,x0,x1,C,x,&al,&dal,&unused);
+ dal *= dxdv;
+ if(mode == 2 || mode == 4 || mode == 6) {
+ al = 125.0;
+ dal = 0.0;
+ }
+
+
+ {
+ double dr0rws;
+ makespline(nx,1,r0rwstab,C);
+ evalspline(nx-1,x0,x1,C,x,&r0rws,&dr0rws,&unused);
+ dr0rws *= dxdv;
+ rws = rws_scale*x;
+ r00 = r0rws * rws;
+ dr00 = dr0rws*rws + r0rws*rws_scale*dxdv;
+ rp = 1.8 * rws;
+ drp = 1.8 * rws_scale*dxdv;
+ }
+
+ makespline(nx,1,evol0tab,C);
+ evalspline(nx-1,x0,x1,C,x,&evol0,&devol0,&unused);
+ devol0 *= dxdv;
+
+ if(1) {
+ printf("%% READPOT PARAMETERS:\n");
+
+ printf("%% ddl = %15.5e %15.5e %15.5e %15.5e\n",ddl[1],ddl[2],ddl[3],ddl[4]);
+ printf("%% anorm3 = %15.5e anorm4 = %15.5e\n",anorm3,anorm4);
+
+ printf("%% x = %15.5e pn = %15.5e\n",x,pn);
+ printf("%% va = %15.5e dva = %15.5e\n",va,dva);
+ printf("%% vb = %15.5e dvb = %15.5e\n",vb,dvb);
+ printf("%% vc = %15.5e dvc = %15.5e\n",vc,dvc);
+ printf("%% vd = %15.5e dvd = %15.5e\n",vd,dvd);
+ printf("%% ve = %15.5e dve = %15.5e\n",ve,dve);
+ printf("%% p1 = %15.5e dp1 = %15.5e\n",p1,dp1);
+ printf("%% al = %15.5e dal = %15.5e\n",al,dal);
+ printf("%% rp = %15.5e drp = %15.5e\n",rp,drp);
+ printf("%% r00= %15.5e dr00= %15.5e\n",r00,dr00);
+ printf("\n");
+ }
+
+ y = new double[nr];
+ dy = new double[nr];
+
+ for(j = 0; j<nr; j++) {
+ double d2y;
+ makespline(nx,nr,&vpairtab[j],C);
+ evalspline(nx-1,x0,x1,C,x,&y[j],&dy[j],&d2y);
+ dy[j] *= dxdv;
+ }
+ vpair_spline = new double[nr-1][4];
+ dvpair_spline = new double[nr-1][4];
+ makespline(nr,1,y,vpair_spline);
+ makespline(nr,1,dy,dvpair_spline);
+
+
+ rcrit = rcrws * rws;
+ rmax = rmrws * rws;
+
+ delete[] dy;
+ delete[] y;
+ delete[] C;
+ delete[] evol0tab;
+ delete[] r0rwstab;
+ delete[] altab;
+ delete[] p1tab;
+ delete[] vetab;
+ delete[] vdtab;
+ delete[] vctab;
+ delete[] vbtab;
+ delete[] vatab;
+}
+
+/*
+int main(int argc,char *argv[]) {
+ double vol = atof(argv[3]);
+ int n = 25,i;
+
+ printf("%% parmin = %s\n%% potin = %s\n%% vol = %15.5e\n",
+ argv[1],argv[2],vol);
+
+ readpot(argv[1],argv[2],vol);
+
+ for(i = 0; i<n; i++) {
+ double x,u,f,vir,dy,d2y;
+
+ x = r0 + i*(r1-r0)/(n-1);
+ evalspline(nr-1,r0,r1,vpair_spline,x,&u,&f,&d2y);
+ evalspline(nr-1,r0,r1,dvpair_spline,x,&vir,&dy,&d2y);
+ printf(" %15.5e %15.5e %15.5e %15.5e\n",
+ x,u,f,vir);
+ }
+
+
+ delete[] dvpair_spline;
+ delete[] vpair_spline;
+
+ return 0;
+}
+*/
diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h
new file mode 100644
index 000000000..c8a7a806d
--- /dev/null
+++ b/src/USER-MGPT/mgpt_readpot.h
@@ -0,0 +1,418 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#ifndef READPOT__
+#define READPOT__
+
+#include <cstdio>
+
+#include "mgpt_splinetab.h"
+
+struct potdata {
+ double va,vb,vc,vd,ve,p1,al,rp,r00,pn;
+ double dva,dvb,dvc,dvd,dve,dp1,dal,drp,dr00;
+ double evol0,devol0;
+ double (*vpair_spline)[4],(*dvpair_spline)[4];
+ double r0,r1;
+ int nr;
+
+ double mass,rcrit,rmax;
+
+ int lang,lmax;
+ double anorm3,anorm4;
+ double ddl[5];
+
+ int ipot,mode;
+ char metal[80];
+
+ double input_vol;
+
+ void readpot(const char *parmin_file,const char *potin_file,double vol);
+
+ void eval_pot(double r,double *e_p,double *f_p) {
+ double d2y;
+ evalspline(nr-1,r0,r1,vpair_spline,r,e_p,f_p,&d2y);
+ }
+
+ void eval_vir(double r,double *v_p) {
+ double dy,d2y;
+ evalspline(nr-1,r0,r1,dvpair_spline,r,v_p,&dy,&d2y);
+ }
+};
+
+
+struct potdata2 {
+ typedef double (*spline)[4];
+ spline va,vb,vc,vd,ve,p1,al,rp,r00;
+ spline dva,dvb,dvc,dvd,dve,dp1,dal,drp,dr00;
+ spline evol0,devol0;
+ double (*vpair)[4][4],(*dvpair)[4][4];
+ double r0,r1,T0,T1;
+ int nr,nt;
+
+ potdata *potlist;
+
+ double mass,rcrit,rmax;
+
+ int lang,lmax;
+ spline ddl[5];
+
+ int ipot,mode;
+ char metal[80];
+
+ double input_vol;
+
+ /* Functions to retrieve temperature dependent parameters */
+
+ double eval_tdep(spline y,double T) {
+ double f,df,d2f;
+
+ if(0) if(T != 3000.0)
+ printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T);
+ evalspline(nt-1,T0,T1,y,T,&f,&df,&d2f);
+ return f;
+ }
+ double eval_tdepderiv(spline y,double T) {
+ double f,df,d2f;
+
+ if(0) if(T != 3000.0)
+ printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T);
+ evalspline(nt-1,T0,T1,y,T,&f,&df,&d2f);
+ return df;
+ }
+
+
+#define make_get(param) \
+ double get_##param(double T) { return eval_tdep(param,T); } \
+ double get_d##param(double T) { return eval_tdep(d##param,T); } \
+ double get_##param##_Tderiv(double T) { return eval_tdepderiv(param,T); }
+
+ /*
+#define make_get(param) \
+ double get_##param(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return potlist[3].param; } \
+ double get_d##param(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return potlist[3].d##param; } \
+ double get_##param##_Tderiv(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return 0.0; }
+ */
+
+ make_get(va) make_get(vb) make_get(vc) make_get(vd) make_get(ve)
+ make_get(p1) make_get(al) make_get(rp) make_get(r00) make_get(evol0)
+#undef make_get
+
+ void get_anorm34(double T,double anorm3_p[1],double anorm4_p[1]) {
+ double
+ s = eval_tdep(ddl[1],T),
+ p = eval_tdep(ddl[2],T),
+ d = eval_tdep(ddl[3],T),
+ f = eval_tdep(ddl[4],T);
+ double ss = s*s, pp = p*p, dd = d*d, ff = f*f;
+ anorm3_p[0] = s*ss + 2.0*( p*pp + d*dd + f*ff);
+ anorm4_p[0] = ss*ss + 2.0*(pp*pp + dd*dd + ff*ff);
+ }
+ double get_anorm3(double T) {
+ double a3,a4;
+ get_anorm34(T,&a3,&a4);
+ return a3;
+ }
+ double get_anorm4(double T) {
+ double a3,a4;
+ get_anorm34(T,&a3,&a4);
+ return a4;
+ }
+ void get_anorm34_Tderiv(double T,double danorm3_p[1],double danorm4_p[1]) {
+ double
+ s = eval_tdep(ddl[1],T), ds = eval_tdepderiv(ddl[1],T),
+ p = eval_tdep(ddl[2],T), dp = eval_tdepderiv(ddl[2],T),
+ d = eval_tdep(ddl[3],T), d_d = eval_tdepderiv(ddl[3],T),
+ f = eval_tdep(ddl[4],T), df = eval_tdepderiv(ddl[4],T);
+ double ss = s*s, pp = p*p, dd = d*d, ff = f*f;
+ danorm3_p[0] = 3.0*ds*ss + 6.0*( dp*pp + d_d*dd + df*ff);
+ danorm4_p[0] = 4.0*ds*s*ss + 8.0*(dp*p*pp + d_d*d*dd + df*f*ff);
+ }
+ double get_anorm3_Tderiv(double T) {
+ double da3,da4;
+ get_anorm34_Tderiv(T,&da3,&da4);
+ return da3;
+ }
+ double get_anorm4_Tderiv(double T) {
+ double da3,da4;
+ get_anorm34_Tderiv(T,&da3,&da4);
+ return da4;
+ }
+
+ /* ... */
+
+
+
+ char * parsefname(const char *nametemplate,int *i0,int *i1,int *stride) {
+ char *s,*p;
+
+ if(0) {
+ s = new char[strlen(nametemplate)+1];
+ } else {
+ int len = 0;
+ while(nametemplate[len] != '\0') len = len + 1;
+ s = new char[len+1];
+ }
+ strcpy(s,nametemplate);
+
+ p = strchr(s,'{');
+ if(p != NULL) {
+ if(sscanf(p+1,"%d:%d:%d",i0,stride,i1) != 3) {
+ fprintf(stderr,"Error in template (\'%s\'), can not parse range.\n",nametemplate);
+ exit(1);
+ }
+ *p = '\0';
+ } else {
+ *i0 = -1;
+ *i1 = -1;
+ *stride = 1;
+ }
+ return s;
+ }
+
+ spline maketempspline(int n,potdata data[],double *ptr) {
+ int stride = &(data[1].va) - &(data[0].va);
+ spline s = new double[n-1][4];
+
+ makespline(n,stride,ptr,s);
+ return s;
+ }
+
+ void readpot2(const char *parmin_template,const char *potin_template,double vol) {
+ int i0,i1,stride,i0x,i1x,stridex;
+ char *parmin_file = parsefname(parmin_template,&i0 ,&i1 ,&stride );
+ char *potin_file = parsefname( potin_template,&i0x,&i1x,&stridex);
+ int ntemp;
+
+ potdata2 &tdeppot = *this;
+
+ if(i0x != i0 || i1x != i1 || stridex != stride) {
+ fprintf(stderr,"Inconsistent templates. parmin_template=\'%s\', potin_template=\'%s\'\n",
+ parmin_template,potin_template);
+ exit(1);
+ }
+ if(i0 < 0 || i1 < i0 || stride <= 0 || (i1-i0)/stride+1 < 4) {
+ fprintf(stderr,"Improper temperature range. Need at least 4 temperature samples. "
+ "i0=%d,i1=%d,stride=%d,basename=\'%s\'\n",
+ i0,i1,stride,parmin_file);
+ exit(1);
+ }
+
+ const char *parmin_suffix = strchr(parmin_template,'}')+1;
+ const char * potin_suffix = strchr( potin_template,'}')+1;
+
+ if(parmin_suffix-1 == NULL) {
+ fprintf(stderr,"No closing }. parmin_template=\'%s\'\n",
+ parmin_template);
+ exit(1);
+ }
+ if(potin_suffix-1 == NULL) {
+ fprintf(stderr,"No closing }. potin_template=\'%s\'\n",
+ potin_template);
+ exit(1);
+ }
+
+ printf("parmin_template = %s\n"
+ "parmin_file = %s\n"
+ "parmin_suffix = %s\n"
+ "T0=%d , T1=%d , stride=%d\n",
+ parmin_template,parmin_file,parmin_suffix,i0,i1,stride);
+
+ ntemp = (i1-i0)/stride + 1;
+ /*potdata **/potlist = new potdata[ntemp];
+ char *parend = parmin_file+strlen(parmin_file);
+ char *potend = potin_file +strlen( potin_file);
+ for(int k=0; k<ntemp; k++) {
+ sprintf(parend,"%d%s",i0+k*stride,parmin_suffix);
+ sprintf(potend,"%d%s",i0+k*stride,potin_suffix);
+
+
+ printf("Calling readpot(%s,%s,%.3f)\n",
+ parmin_file,potin_file,vol);
+ potlist[k].readpot(parmin_file,potin_file,vol);
+
+ if(k > 0) {
+ if(potlist[k].nr != potlist[k-1].nr) {
+ fprintf(stderr,"nr differs between file %d and %d. Exiting.\n",
+ k,k-1);
+ exit(1);
+ }
+
+ if(potlist[k].r0 != potlist[k-1].r0) {
+ fprintf(stderr,"r0 differs between file %d and %d. Exiting.\n",
+ k,k-1);
+ exit(1);
+ }
+
+ if(potlist[k].r1 != potlist[k-1].r1) {
+ fprintf(stderr,"r1 differs between file %d and %d. Exiting.\n",
+ k,k-1);
+ exit(1);
+ }
+ }
+ }
+ tdeppot.r0 = potlist[0].r0;
+ tdeppot.r1 = potlist[0].r1;
+ tdeppot.nr = potlist[0].nr;
+ tdeppot.T0 = i0;
+ tdeppot.T1 = i1;
+ tdeppot.nt = ntemp;
+
+ tdeppot.mass = potlist[0].mass;
+ tdeppot.rcrit = potlist[0].rcrit;
+ tdeppot.rmax = potlist[0].rmax;
+
+ tdeppot.lang = potlist[0].lang;
+ tdeppot.lmax = potlist[0].lmax;
+ tdeppot.ipot = potlist[0].ipot;
+ tdeppot.mode = potlist[0].mode;
+ tdeppot.input_vol = potlist[0].input_vol;
+
+ strncpy(tdeppot.metal,potlist[0].metal,sizeof(tdeppot.metal)/sizeof(char));
+ tdeppot.metal[sizeof(tdeppot.metal)/sizeof(char) - 1] = '\0';
+
+ delete[] parmin_file;
+ delete[] potin_file;
+
+ // Base parameters
+ tdeppot.va = maketempspline(ntemp,potlist,&(potlist[0].va));
+ tdeppot.vb = maketempspline(ntemp,potlist,&(potlist[0].vb));
+ tdeppot.vc = maketempspline(ntemp,potlist,&(potlist[0].vc));
+ tdeppot.vd = maketempspline(ntemp,potlist,&(potlist[0].vd));
+ tdeppot.ve = maketempspline(ntemp,potlist,&(potlist[0].ve));
+
+ tdeppot.p1 = maketempspline(ntemp,potlist,&(potlist[0].p1));
+ tdeppot.al = maketempspline(ntemp,potlist,&(potlist[0].al));
+ tdeppot.rp = maketempspline(ntemp,potlist,&(potlist[0].rp));
+ tdeppot.r00 = maketempspline(ntemp,potlist,&(potlist[0].r00));
+
+ tdeppot.evol0 = maketempspline(ntemp,potlist,&(potlist[0].evol0));
+
+ // Volume derivatives of base parameters
+ tdeppot.dva = maketempspline(ntemp,potlist,&(potlist[0].dva));
+ tdeppot.dvb = maketempspline(ntemp,potlist,&(potlist[0].dvb));
+ tdeppot.dvc = maketempspline(ntemp,potlist,&(potlist[0].dvc));
+ tdeppot.dvd = maketempspline(ntemp,potlist,&(potlist[0].dvd));
+ tdeppot.dve = maketempspline(ntemp,potlist,&(potlist[0].dve));
+
+ tdeppot.dp1 = maketempspline(ntemp,potlist,&(potlist[0].dp1));
+ tdeppot.dal = maketempspline(ntemp,potlist,&(potlist[0].dal));
+ tdeppot.drp = maketempspline(ntemp,potlist,&(potlist[0].drp));
+ tdeppot.dr00 = maketempspline(ntemp,potlist,&(potlist[0].dr00));
+
+ tdeppot.devol0 = maketempspline(ntemp,potlist,&(potlist[0].devol0));
+
+
+ tdeppot.ddl[0] = 0;
+ for(int k = 1; k<=4; k++)
+ tdeppot.ddl[k] = maketempspline(ntemp,potlist,&(potlist[0].ddl[k]));
+
+ {
+ double *v = new double[ntemp];
+ double (*C)[4] = new double[ntemp-1][4];
+
+ int sz = (nr-1)*(ntemp-1);
+ //printf("Allocation:: nr=%d ntemp=%d size=%d\n",nr,ntemp,sz);
+ tdeppot.vpair = new double[sz][4][4];
+ tdeppot.dvpair = new double[sz][4][4];
+ /*
+ printf("vpair = %llx , dvpair = %llx",
+ (unsigned long long int) tdeppot.vpair,
+ (unsigned long long int) tdeppot.dvpair);
+ printf(" @@@@@@@@@@@@@@ nr = %d\n",nr);
+ */
+ for(int i = 0; i<nr-1; i++)
+ for(int j = 0; j<4; j++) {
+ /*
+ if(j == 5)
+ printf(" ############### i=%d\n",i);
+ */
+
+ /* Make pair interaction interpolation functions */
+ for(int k = 0; k<ntemp; k++) {
+ if(0) if(i >= potlist[k].nr-1)
+ printf("Index error, local_nr=%d, k=%d, i=%d, nr=%d\n",nr,k,i,potlist[k].nr);
+ v[k] = potlist[k].vpair_spline[i][j];
+ }
+ makespline(ntemp,1,v,C);
+
+ for(int k = 0; k<ntemp-1; k++)
+ for(int m = 0; m<4; m++)
+ tdeppot.vpair[k*(nr-1) + i][j][m] = C[k][m];
+
+ /* Make pair virial interpolation functions */
+ for(int k = 0; k<ntemp; k++)
+ v[k] = potlist[k].dvpair_spline[i][j];
+ makespline(ntemp,1,v,C);
+
+ for(int k = 0; k<ntemp-1; k++)
+ for(int m = 0; m<4; m++)
+ tdeppot.dvpair[k*(nr-1) + i][j][m] = C[k][m];
+
+ }
+
+ delete[] C;
+ delete[] v;
+ }
+
+ }
+
+ void eval2Dspline(double fun[][4][4],double r,double T,double *e_p,double *f_p,double *dedT_p) {
+ double C[4],dC[4],dd;
+ double Tfrac = (T-T0)/(T1-T0) * (nt-1);
+ double rfrac = (r-r0)/(r1-r0) * (nr-1);
+ int k = (int) Tfrac;
+ int i = (int) rfrac;
+ int j;
+
+ if(k < 0) k = 0;
+ else if(k > nt-2) k = nt-2;
+
+ if(i < 0) i = 0;
+ else if(i > nr-2) i = nr-2;
+
+ /*
+ printf("eval_pot nr=%d nt=%d\n",nr,nt);
+ printf("eval_pot r=%.3f T=%.3f k=%d i=%d\n",
+ r,T,k,i);
+ printf("Tfrac=%.3f Tfrac-k=%.3f\n",Tfrac,Tfrac-k);
+ printf("rfrac=%.3f rfrac-i=%.3f\n",rfrac,rfrac-i);
+ */
+ for(j = 0; j<4; j++) {
+ evalcubic(fun[k*(nr-1) + i][j],Tfrac-k,&C[j],&dC[j],&dd);
+ dC[j] = dC[j] * ((nt-1) / (T1-T0));
+ }
+ /*
+ printf("C coeff: %.3e %.3e %.3e %.3e\n",
+ C[0],C[1],C[2],C[3]);
+ */
+ evalcubic(C,rfrac-i,e_p,f_p,&dd);
+ evalcubic(dC,rfrac-i,dedT_p,&dd,&dd);
+ *f_p *= (nr-1) / (r1-r0);
+ }
+ void eval_pot(double r,double T,double *e_p,double *f_p,double *dedT_p) {
+ eval2Dspline(vpair,r,T,e_p,f_p,dedT_p);
+ }
+ void eval_vir(double r,double T,double *v_p) {
+ double vf,dvdT;
+ eval2Dspline(dvpair,r,T,v_p,&vf,&dvdT);
+ }
+};
+
+
+#endif
diff --git a/src/USER-MGPT/mgpt_splinetab.cpp b/src/USER-MGPT/mgpt_splinetab.cpp
new file mode 100644
index 000000000..22df495f9
--- /dev/null
+++ b/src/USER-MGPT/mgpt_splinetab.cpp
@@ -0,0 +1,125 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include "mgpt_splinetab.h"
+
+static void trisolve(int n,double A[][3],double y[]) {
+ /* Backward elimination */
+ for(int i = n-1; i>0; i--) {
+ double q = A[i-1][2] / A[i][1];
+ A[i-1][1] = A[i-1][1] - q*A[i][0];
+ y[i-1] = y[i-1] - q*y[i];
+ }
+
+ /* Forward substitution */
+ y[0] = y[0] / A[0][1];
+ for(int i = 1; i<n; i++)
+ y[i] = (y[i] - A[i][0]*y[i-1]) / A[i][1];
+}
+
+void makespline(int ntab,int stride,double tab[],double C[][4]) {
+ int n = 3*(ntab-1);
+
+ double (*A)[3] = new double[n][3];
+ double *y = new double[n];
+
+ double h_left,h_right,d;
+ int i,j;
+
+ /* Second order second derivative approximation
+ at end points. */
+ h_left =
+ 2.0*tab[stride*0] - 5.0*tab[stride*1] +
+ 4.0*tab[stride*2] - 1.0*tab[stride*3];
+ h_right =
+ 2.0*tab[stride*(ntab-1)] - 5.0*tab[stride*(ntab-2)] +
+ 4.0*tab[stride*(ntab-3)] - 1.0*tab[stride*(ntab-4)];
+
+ A[0][0] = 0.0; A[0][1] = 0.0; A[0][2] = 2.0; y[0] = h_left;
+ for(i = 1; i<ntab-1; i++) {
+ j = 3*(i-1);
+ d = tab[stride*i] - tab[stride*(i-1)];
+ A[j+1][0] = 1.0; A[j+1][1] = 1.0; A[j+1][2] = 1.0; y[j+1] = d;
+ A[j+2][0] = 1.0; A[j+2][1] = 2.0; A[j+2][2] = -1.0; y[j+2] = -d;
+ A[j+3][0] = 2.0; A[j+3][1] = 2.0; A[j+3][2] = -2.0; y[j+3] = 2.0*d;
+ }
+
+ j = 3*(ntab-2);
+ d = tab[stride*(ntab-1)] - tab[stride*(ntab-2)];
+ A[j+1][0] = 1.0; A[j+1][1] = 1.0; A[j+1][2] = 1.0; y[j+1] = d;
+ A[j+2][0] = 2.0; A[j+2][1] = 6.0; A[j+2][2] = 0.0; y[j+2] = h_right;
+
+ trisolve(n,A,y);
+
+ for(i = 0; i<ntab-1; i++) {
+ C[i][0] = tab[stride*i];
+ C[i][1] = y[3*i+0];
+ C[i][2] = y[3*i+1];
+ C[i][3] = y[3*i+2];
+ }
+
+ delete[] y;
+ delete[] A;
+}
+
+void evalcubic(double p[4],double x,double *y,double *dy,double *d2y) {
+ double t1,t2,t3;
+
+ t1 = p[2] + x*p[3];
+ t2 = p[1] + x*t1;
+
+ t3 = t1 + x*p[3];
+
+ *y = p[0] + x*t2;
+ *dy = (t2 + x*t3);
+ *d2y = 2.0*(t3 + x*p[3]);
+}
+
+void evalspline(int n,double x0,double x1,double C[][4],
+ double x,double *y,double *dy,double *d2y) {
+ double xhat,t1,t2,t3;
+ double *p;
+ int idx;
+ double dxinv = n/(x1-x0);
+ xhat = (x-x0)/(x1-x0) * n;
+
+ idx = (int) xhat;
+ if(idx < 0) idx = 0;
+ if(idx > n-1) idx = n-1;
+ xhat = xhat - idx;
+ p = C[idx];
+
+ if(0) {
+ *y = p[0] + xhat*(p[1] + xhat*(p[2] + xhat*p[3]));
+
+ *dy = p[1] + xhat*(2*p[2] + xhat*3*p[3]);
+ *d2y = 2*p[2] + xhat*6*p[3];
+
+ *dy *= dxinv;
+ *d2y *= dxinv*dxinv;
+ } else {
+ t1 = p[2] + xhat*p[3];
+ t2 = p[1] + xhat*t1;
+
+ t3 = t1 + xhat*p[3];
+
+ *y = p[0] + xhat*t2;
+ *dy = (t2 + xhat*t3)*dxinv;
+ *d2y = 2.0*(t3 + xhat*p[3])*(dxinv*dxinv);
+ }
+}
diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/USER-MGPT/mgpt_splinetab.h
new file mode 100644
index 000000000..e719f3421
--- /dev/null
+++ b/src/USER-MGPT/mgpt_splinetab.h
@@ -0,0 +1,62 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#ifndef SPLINETAB__
+#define SPLINETAB__
+
+
+/*
+ Given a table of ntab data points tab, assumed to be sampled
+ on an equidistant grid, compute coefficients of interpolating
+ cubic polynimials, one per interval (i.e. ntab-1 polynomials).
+
+ Input point i is located at tab[i*stride].
+
+ Coefficients of output polynomial j are at C[j][0..3];
+
+ The piecewise polynimials form a C^2 function which
+ approximates the input function to fourth order.
+
+ The computational cost of this routine is O(ntab).
+*/
+void makespline(int ntab,int stride,double tab[],double C[][4]);
+
+
+/*
+ Evaluate the spline function with coefficients in C (as returned
+ by makespline()) in point x.
+ x0 and x1 are the end points of the x points corresponding to
+ original input interval tab of makespline(). n is ntab-1.
+
+ The output is the value (y) of the interpolating spline, and the
+ first (dy) and second (d2y) dervatives.
+
+ The computational cost of this routine is O(1).
+*/
+void evalspline(int n,double x0,double x1,double C[][4],
+ double x,double *y,double *dy,double *d2y);
+
+
+/* Evaluate cubic polynomial represented by p in point x.
+ The first and second derivatives are also returned.
+ This can be used to evaluate one of the sub-polynomials
+ in a spline. */
+void evalcubic(double p[4],double x,double *y,double *dy,double *d2y);
+
+#endif
+
diff --git a/src/USER-MGPT/mgpt_ttr_5022.c.h b/src/USER-MGPT/mgpt_ttr_5022.c.h
new file mode 100644
index 000000000..2b697c6b8
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_5022.c.h
@@ -0,0 +1,202 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+#include <pmmintrin.h>
+
+void ttr_5_8_3_v2r2(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+__m128d Areg1,Areg2;
+__m128d B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2;
+__m128d T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2;
+
+Areg1 = _mm_load_pd(&A[0]) ;
+T0reg1 = _mm_load_pd(&B0[0]) ;
+T1reg1 = _mm_load_pd(&B1[0]) ;
+T2reg1 = _mm_load_pd(&B2[0]) ;
+T0reg1 = _mm_mul_pd(T0reg1,Areg1) ;
+T1reg1 = _mm_mul_pd(T1reg1,Areg1) ;
+T2reg1 = _mm_mul_pd(T2reg1,Areg1) ;
+
+Areg2 = _mm_load_pd(&A[2]) ;
+T0reg2 = _mm_load_pd(&B0[2]) ;
+T1reg2 = _mm_load_pd(&B1[2]) ;
+T2reg2 = _mm_load_pd(&B2[2]) ;
+T0reg2 = _mm_mul_pd(T0reg2,Areg2) ;
+T1reg2 = _mm_mul_pd(T1reg2,Areg2) ;
+T2reg2 = _mm_mul_pd(T2reg2,Areg2) ;
+
+Areg1 = _mm_load_pd(&A[4]) ;
+B0reg1 = _mm_load_pd(&B0[4]) ;
+B1reg1 = _mm_load_pd(&B1[4]) ;
+B2reg1 = _mm_load_pd(&B2[4]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[8]) ;
+B0reg2 = _mm_load_pd(&B0[8]) ;
+B1reg2 = _mm_load_pd(&B1[8]) ;
+B2reg2 = _mm_load_pd(&B2[8]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[10]) ;
+B0reg1 = _mm_load_pd(&B0[10]) ;
+B1reg1 = _mm_load_pd(&B1[10]) ;
+B2reg1 = _mm_load_pd(&B2[10]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[12]) ;
+B0reg2 = _mm_load_pd(&B0[12]) ;
+B1reg2 = _mm_load_pd(&B1[12]) ;
+B2reg2 = _mm_load_pd(&B2[12]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[16]) ;
+B0reg1 = _mm_load_pd(&B0[16]) ;
+B1reg1 = _mm_load_pd(&B1[16]) ;
+B2reg1 = _mm_load_pd(&B2[16]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[18]) ;
+B0reg2 = _mm_load_pd(&B0[18]) ;
+B1reg2 = _mm_load_pd(&B1[18]) ;
+B2reg2 = _mm_load_pd(&B2[18]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[20]) ;
+B0reg1 = _mm_load_pd(&B0[20]) ;
+B1reg1 = _mm_load_pd(&B1[20]) ;
+B2reg1 = _mm_load_pd(&B2[20]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[24]) ;
+B0reg2 = _mm_load_pd(&B0[24]) ;
+B1reg2 = _mm_load_pd(&B1[24]) ;
+B2reg2 = _mm_load_pd(&B2[24]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[26]) ;
+B0reg1 = _mm_load_pd(&B0[26]) ;
+B1reg1 = _mm_load_pd(&B1[26]) ;
+B2reg1 = _mm_load_pd(&B2[26]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[28]) ;
+B0reg2 = _mm_load_pd(&B0[28]) ;
+B1reg2 = _mm_load_pd(&B1[28]) ;
+B2reg2 = _mm_load_pd(&B2[28]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[32]) ;
+B0reg1 = _mm_load_pd(&B0[32]) ;
+B1reg1 = _mm_load_pd(&B1[32]) ;
+B2reg1 = _mm_load_pd(&B2[32]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[34]) ;
+B0reg2 = _mm_load_pd(&B0[34]) ;
+B1reg2 = _mm_load_pd(&B1[34]) ;
+B2reg2 = _mm_load_pd(&B2[34]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[36]) ;
+B0reg1 = _mm_load_pd(&B0[36]) ;
+B1reg1 = _mm_load_pd(&B1[36]) ;
+B2reg1 = _mm_load_pd(&B2[36]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+
+T0reg1 = _mm_add_pd(T0reg1,T0reg2) ;
+T1reg1 = _mm_add_pd(T1reg1,T1reg2) ;
+T2reg1 = _mm_add_pd(T2reg1,T2reg2) ;
+
+T0reg1 = _mm_hadd_pd(T0reg1,T0reg1) ;
+_mm_store_sd(tout0,T0reg1) ;
+T1reg1 = _mm_hadd_pd(T1reg1,T1reg1) ;
+_mm_store_sd(tout1,T1reg1) ;
+T2reg1 = _mm_hadd_pd(T2reg1,T2reg1) ;
+_mm_store_sd(tout2,T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_5042.c.h b/src/USER-MGPT/mgpt_ttr_5042.c.h
new file mode 100644
index 000000000..4d77a49c9
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_5042.c.h
@@ -0,0 +1,150 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+#include <pmmintrin.h>
+
+void ttr_5_8_3_v4r2(const float * restrict A,
+ const float * restrict B0,float * restrict tout0,
+ const float * restrict B1,float * restrict tout1,
+ const float * restrict B2,float * restrict tout2) {
+__m128 Areg1,Areg2;
+__m128 B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2;
+__m128 T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2;
+
+Areg1 = _mm_load_ps(&A[0]) ;
+T0reg1 = _mm_load_ps(&B0[0]) ;
+T1reg1 = _mm_load_ps(&B1[0]) ;
+T2reg1 = _mm_load_ps(&B2[0]) ;
+T0reg1 = _mm_mul_ps(T0reg1,Areg1) ;
+T1reg1 = _mm_mul_ps(T1reg1,Areg1) ;
+T2reg1 = _mm_mul_ps(T2reg1,Areg1) ;
+
+Areg2 = _mm_load_ps(&A[4]) ;
+T0reg2 = _mm_load_ps(&B0[4]) ;
+T1reg2 = _mm_load_ps(&B1[4]) ;
+T2reg2 = _mm_load_ps(&B2[4]) ;
+T0reg2 = _mm_mul_ps(T0reg2,Areg2) ;
+T1reg2 = _mm_mul_ps(T1reg2,Areg2) ;
+T2reg2 = _mm_mul_ps(T2reg2,Areg2) ;
+
+Areg1 = _mm_load_ps(&A[8]) ;
+B0reg1 = _mm_load_ps(&B0[8]) ;
+B1reg1 = _mm_load_ps(&B1[8]) ;
+B2reg1 = _mm_load_ps(&B2[8]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[12]) ;
+B0reg2 = _mm_load_ps(&B0[12]) ;
+B1reg2 = _mm_load_ps(&B1[12]) ;
+B2reg2 = _mm_load_ps(&B2[12]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[16]) ;
+B0reg1 = _mm_load_ps(&B0[16]) ;
+B1reg1 = _mm_load_ps(&B1[16]) ;
+B2reg1 = _mm_load_ps(&B2[16]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[20]) ;
+B0reg2 = _mm_load_ps(&B0[20]) ;
+B1reg2 = _mm_load_ps(&B1[20]) ;
+B2reg2 = _mm_load_ps(&B2[20]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[24]) ;
+B0reg1 = _mm_load_ps(&B0[24]) ;
+B1reg1 = _mm_load_ps(&B1[24]) ;
+B2reg1 = _mm_load_ps(&B2[24]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[28]) ;
+B0reg2 = _mm_load_ps(&B0[28]) ;
+B1reg2 = _mm_load_ps(&B1[28]) ;
+B2reg2 = _mm_load_ps(&B2[28]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[32]) ;
+B0reg1 = _mm_load_ps(&B0[32]) ;
+B1reg1 = _mm_load_ps(&B1[32]) ;
+B2reg1 = _mm_load_ps(&B2[32]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[36]) ;
+B0reg2 = _mm_load_ps(&B0[36]) ;
+B1reg2 = _mm_load_ps(&B1[36]) ;
+B2reg2 = _mm_load_ps(&B2[36]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+
+T0reg1 = _mm_add_ps(T0reg1,T0reg2) ;
+T1reg1 = _mm_add_ps(T1reg1,T1reg2) ;
+T2reg1 = _mm_add_ps(T2reg1,T2reg2) ;
+
+T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ;
+T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ;
+_mm_store_ss(tout0,T0reg1) ;
+T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ;
+T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ;
+_mm_store_ss(tout1,T1reg1) ;
+T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ;
+T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ;
+_mm_store_ss(tout2,T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_5123.c.h b/src/USER-MGPT/mgpt_ttr_5123.c.h
new file mode 100644
index 000000000..e8237f4eb
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_5123.c.h
@@ -0,0 +1,245 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+
+//#define TESTING
+
+#ifdef TESTING
+
+typedef struct {
+ double x,y;
+} pair;
+
+
+#define CPLX pair
+
+static double my_creal(CPLX x) {
+ return ((double *) &x)[0];
+}
+static double my_cimag(CPLX x) {
+ return ((double *) &x)[1];
+}
+static CPLX my_lfpd(const double *p) {
+ return ((CPLX *) p)[0];
+}
+
+/*
+// Not needed for trace calculations.
+static void my_stfpd(double *p,CPLX x) {
+ ((CPLX *) p)[0] = x;
+}
+static CPLX my_fxsmul(CPLX x,double a) {
+ double y[2];
+ y[0] = a * my_creal(x);
+ y[1] = a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) {
+ double y[2];
+ y[0] = my_creal(t) + a * my_creal(x);
+ y[1] = my_cimag(t) + a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+*/
+
+static CPLX my_fpmul(CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(y) * my_creal(x);
+ U.z[1] = my_cimag(y) * my_cimag(x);
+ return U.c;
+}
+static CPLX my_fpadd(CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(y) + my_creal(x);
+ U.z[1] = my_cimag(y) + my_cimag(x);
+ return U.c;
+}
+static CPLX my_fpmadd(CPLX t,CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(t) + my_creal(y) * my_creal(x);
+ U.z[1] = my_cimag(t) + my_cimag(y) * my_cimag(x);
+ return U.c;
+}
+
+#define __creal my_creal
+#define __cimag my_cimag
+#define __lfpd my_lfpd
+#define __stfpd my_stfpd
+#define __fxsmul my_fxsmul
+#define __fxcpmadd my_fxcpmadd
+
+#define __fpadd my_fpadd
+#define __fpmul my_fpmul
+#define __fpmadd my_fpmadd
+
+#else
+
+#define CPLX double _Complex
+
+#endif
+
+void ttr_bg_5_8_3_v2r3(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+CPLX Areg1,Areg2,Areg3;
+CPLX B0reg1,B0reg2,B0reg3,B1reg1,B1reg2,B1reg3,B2reg1,B2reg2,B2reg3;
+CPLX T0reg1,T0reg2,T0reg3,T1reg1,T1reg2,T1reg3,T2reg1,T2reg2,T2reg3;
+
+Areg1 = __lfpd(&A[0]) ;
+B0reg1 = __lfpd(&B0[0]) ;
+B1reg1 = __lfpd(&B1[0]) ;
+B2reg1 = __lfpd(&B2[0]) ;
+T0reg1 = __fpmul(Areg1,B0reg1) ;
+T1reg1 = __fpmul(Areg1,B1reg1) ;
+T2reg1 = __fpmul(Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[2]) ;
+B0reg2 = __lfpd(&B0[2]) ;
+B1reg2 = __lfpd(&B1[2]) ;
+B2reg2 = __lfpd(&B2[2]) ;
+T0reg2 = __fpmul(Areg2,B0reg2) ;
+T1reg2 = __fpmul(Areg2,B1reg2) ;
+T2reg2 = __fpmul(Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[4]) ;
+B0reg3 = __lfpd(&B0[4]) ;
+B1reg3 = __lfpd(&B1[4]) ;
+B2reg3 = __lfpd(&B2[4]) ;
+T0reg3 = __fpmul(Areg3,B0reg3) ;
+T1reg3 = __fpmul(Areg3,B1reg3) ;
+T2reg3 = __fpmul(Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[8]) ;
+B0reg1 = __lfpd(&B0[8]) ;
+B1reg1 = __lfpd(&B1[8]) ;
+B2reg1 = __lfpd(&B2[8]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[10]) ;
+B0reg2 = __lfpd(&B0[10]) ;
+B1reg2 = __lfpd(&B1[10]) ;
+B2reg2 = __lfpd(&B2[10]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[12]) ;
+B0reg3 = __lfpd(&B0[12]) ;
+B1reg3 = __lfpd(&B1[12]) ;
+B2reg3 = __lfpd(&B2[12]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[16]) ;
+B0reg1 = __lfpd(&B0[16]) ;
+B1reg1 = __lfpd(&B1[16]) ;
+B2reg1 = __lfpd(&B2[16]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[18]) ;
+B0reg2 = __lfpd(&B0[18]) ;
+B1reg2 = __lfpd(&B1[18]) ;
+B2reg2 = __lfpd(&B2[18]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[20]) ;
+B0reg3 = __lfpd(&B0[20]) ;
+B1reg3 = __lfpd(&B1[20]) ;
+B2reg3 = __lfpd(&B2[20]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[24]) ;
+B0reg1 = __lfpd(&B0[24]) ;
+B1reg1 = __lfpd(&B1[24]) ;
+B2reg1 = __lfpd(&B2[24]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[26]) ;
+B0reg2 = __lfpd(&B0[26]) ;
+B1reg2 = __lfpd(&B1[26]) ;
+B2reg2 = __lfpd(&B2[26]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[28]) ;
+B0reg3 = __lfpd(&B0[28]) ;
+B1reg3 = __lfpd(&B1[28]) ;
+B2reg3 = __lfpd(&B2[28]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[32]) ;
+B0reg1 = __lfpd(&B0[32]) ;
+B1reg1 = __lfpd(&B1[32]) ;
+B2reg1 = __lfpd(&B2[32]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[34]) ;
+B0reg2 = __lfpd(&B0[34]) ;
+B1reg2 = __lfpd(&B1[34]) ;
+B2reg2 = __lfpd(&B2[34]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[36]) ;
+B0reg3 = __lfpd(&B0[36]) ;
+B1reg3 = __lfpd(&B1[36]) ;
+B2reg3 = __lfpd(&B2[36]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+
+T0reg1 = __fpadd(T0reg1,T0reg2) ;
+T1reg1 = __fpadd(T1reg1,T1reg2) ;
+T2reg1 = __fpadd(T2reg1,T2reg2) ;
+T0reg1 = __fpadd(T0reg1,T0reg3) ;
+T1reg1 = __fpadd(T1reg1,T1reg3) ;
+T2reg1 = __fpadd(T2reg1,T2reg3) ;
+
+*tout0 = __creal(T0reg1) + __cimag(T0reg1) ;
+*tout1 = __creal(T1reg1) + __cimag(T1reg1) ;
+*tout2 = __creal(T2reg1) + __cimag(T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_5141.c.h b/src/USER-MGPT/mgpt_ttr_5141.c.h
new file mode 100644
index 000000000..d77c6935f
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_5141.c.h
@@ -0,0 +1,142 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#define vector vector4double
+#define my_vec_add(a,b) vec_add(a,b)
+#define my_vec_mul(a,b) vec_mul(a,b)
+#define my_vec_fma(a,b,c) vec_madd(b,c,a)
+#define my_vec_ld(ptr) vec_lda(0,ptr)
+#define my_vec_sldw(x,y,n) vec_sldw(x,y,n)
+#define my_vec_sts(x,ptr) vec_sts(x,0,ptr)
+
+#define const
+#define real double
+
+void ttr_bg_5_8_3_v4r1(const real * restrict A,
+ const real * restrict B0,real * restrict tout0,
+ const real * restrict B1,real * restrict tout1,
+ const real * restrict B2,real * restrict tout2) {
+vector Areg1;
+vector B0reg1,B1reg1,B2reg1;
+vector T0reg1,T1reg1,T2reg1;
+
+Areg1 = my_vec_ld(&A[0]) ;
+B0reg1 = my_vec_ld(&B0[0]) ;
+B1reg1 = my_vec_ld(&B1[0]) ;
+B2reg1 = my_vec_ld(&B2[0]) ;
+T0reg1 = my_vec_mul(Areg1,B0reg1) ;
+T1reg1 = my_vec_mul(Areg1,B1reg1) ;
+T2reg1 = my_vec_mul(Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[4]) ;
+B0reg1 = my_vec_ld(&B0[4]) ;
+B1reg1 = my_vec_ld(&B1[4]) ;
+B2reg1 = my_vec_ld(&B2[4]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[8]) ;
+B0reg1 = my_vec_ld(&B0[8]) ;
+B1reg1 = my_vec_ld(&B1[8]) ;
+B2reg1 = my_vec_ld(&B2[8]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[12]) ;
+B0reg1 = my_vec_ld(&B0[12]) ;
+B1reg1 = my_vec_ld(&B1[12]) ;
+B2reg1 = my_vec_ld(&B2[12]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[16]) ;
+B0reg1 = my_vec_ld(&B0[16]) ;
+B1reg1 = my_vec_ld(&B1[16]) ;
+B2reg1 = my_vec_ld(&B2[16]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[20]) ;
+B0reg1 = my_vec_ld(&B0[20]) ;
+B1reg1 = my_vec_ld(&B1[20]) ;
+B2reg1 = my_vec_ld(&B2[20]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[24]) ;
+B0reg1 = my_vec_ld(&B0[24]) ;
+B1reg1 = my_vec_ld(&B1[24]) ;
+B2reg1 = my_vec_ld(&B2[24]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[28]) ;
+B0reg1 = my_vec_ld(&B0[28]) ;
+B1reg1 = my_vec_ld(&B1[28]) ;
+B2reg1 = my_vec_ld(&B2[28]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[32]) ;
+B0reg1 = my_vec_ld(&B0[32]) ;
+B1reg1 = my_vec_ld(&B1[32]) ;
+B2reg1 = my_vec_ld(&B2[32]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[36]) ;
+B0reg1 = my_vec_ld(&B0[36]) ;
+B1reg1 = my_vec_ld(&B1[36]) ;
+B2reg1 = my_vec_ld(&B2[36]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+
+
+T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,2));
+T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,1));
+my_vec_sts(T0reg1,tout0);
+T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,2));
+T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,1));
+my_vec_sts(T1reg1,tout1);
+T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,2));
+T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,1));
+my_vec_sts(T2reg1,tout2);
+
+}
+
+
+#undef vector
+#undef my_vec_add
+#undef my_vec_mul
+#undef my_vec_fma
+#undef my_vec_ld
+#undef my_vec_sldw
+#undef my_vec_sts
+
+#undef const
+#undef real
diff --git a/src/USER-MGPT/mgpt_ttr_7022.c.h b/src/USER-MGPT/mgpt_ttr_7022.c.h
new file mode 100644
index 000000000..99aeaec50
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_7022.c.h
@@ -0,0 +1,345 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+#include <pmmintrin.h>
+
+void ttr_7_8_3_v2r2(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+__m128d Areg1,Areg2;
+__m128d B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2;
+__m128d T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2;
+
+Areg1 = _mm_load_pd(&A[0]) ;
+T0reg1 = _mm_load_pd(&B0[0]) ;
+T1reg1 = _mm_load_pd(&B1[0]) ;
+T2reg1 = _mm_load_pd(&B2[0]) ;
+T0reg1 = _mm_mul_pd(T0reg1,Areg1) ;
+T1reg1 = _mm_mul_pd(T1reg1,Areg1) ;
+T2reg1 = _mm_mul_pd(T2reg1,Areg1) ;
+
+Areg2 = _mm_load_pd(&A[2]) ;
+T0reg2 = _mm_load_pd(&B0[2]) ;
+T1reg2 = _mm_load_pd(&B1[2]) ;
+T2reg2 = _mm_load_pd(&B2[2]) ;
+T0reg2 = _mm_mul_pd(T0reg2,Areg2) ;
+T1reg2 = _mm_mul_pd(T1reg2,Areg2) ;
+T2reg2 = _mm_mul_pd(T2reg2,Areg2) ;
+
+Areg1 = _mm_load_pd(&A[4]) ;
+B0reg1 = _mm_load_pd(&B0[4]) ;
+B1reg1 = _mm_load_pd(&B1[4]) ;
+B2reg1 = _mm_load_pd(&B2[4]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[6]) ;
+B0reg2 = _mm_load_pd(&B0[6]) ;
+B1reg2 = _mm_load_pd(&B1[6]) ;
+B2reg2 = _mm_load_pd(&B2[6]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[8]) ;
+B0reg1 = _mm_load_pd(&B0[8]) ;
+B1reg1 = _mm_load_pd(&B1[8]) ;
+B2reg1 = _mm_load_pd(&B2[8]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[10]) ;
+B0reg2 = _mm_load_pd(&B0[10]) ;
+B1reg2 = _mm_load_pd(&B1[10]) ;
+B2reg2 = _mm_load_pd(&B2[10]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[12]) ;
+B0reg1 = _mm_load_pd(&B0[12]) ;
+B1reg1 = _mm_load_pd(&B1[12]) ;
+B2reg1 = _mm_load_pd(&B2[12]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[14]) ;
+B0reg2 = _mm_load_pd(&B0[14]) ;
+B1reg2 = _mm_load_pd(&B1[14]) ;
+B2reg2 = _mm_load_pd(&B2[14]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[16]) ;
+B0reg1 = _mm_load_pd(&B0[16]) ;
+B1reg1 = _mm_load_pd(&B1[16]) ;
+B2reg1 = _mm_load_pd(&B2[16]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[18]) ;
+B0reg2 = _mm_load_pd(&B0[18]) ;
+B1reg2 = _mm_load_pd(&B1[18]) ;
+B2reg2 = _mm_load_pd(&B2[18]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[20]) ;
+B0reg1 = _mm_load_pd(&B0[20]) ;
+B1reg1 = _mm_load_pd(&B1[20]) ;
+B2reg1 = _mm_load_pd(&B2[20]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[22]) ;
+B0reg2 = _mm_load_pd(&B0[22]) ;
+B1reg2 = _mm_load_pd(&B1[22]) ;
+B2reg2 = _mm_load_pd(&B2[22]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[24]) ;
+B0reg1 = _mm_load_pd(&B0[24]) ;
+B1reg1 = _mm_load_pd(&B1[24]) ;
+B2reg1 = _mm_load_pd(&B2[24]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[26]) ;
+B0reg2 = _mm_load_pd(&B0[26]) ;
+B1reg2 = _mm_load_pd(&B1[26]) ;
+B2reg2 = _mm_load_pd(&B2[26]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[28]) ;
+B0reg1 = _mm_load_pd(&B0[28]) ;
+B1reg1 = _mm_load_pd(&B1[28]) ;
+B2reg1 = _mm_load_pd(&B2[28]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[30]) ;
+B0reg2 = _mm_load_pd(&B0[30]) ;
+B1reg2 = _mm_load_pd(&B1[30]) ;
+B2reg2 = _mm_load_pd(&B2[30]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[32]) ;
+B0reg1 = _mm_load_pd(&B0[32]) ;
+B1reg1 = _mm_load_pd(&B1[32]) ;
+B2reg1 = _mm_load_pd(&B2[32]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[34]) ;
+B0reg2 = _mm_load_pd(&B0[34]) ;
+B1reg2 = _mm_load_pd(&B1[34]) ;
+B2reg2 = _mm_load_pd(&B2[34]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[36]) ;
+B0reg1 = _mm_load_pd(&B0[36]) ;
+B1reg1 = _mm_load_pd(&B1[36]) ;
+B2reg1 = _mm_load_pd(&B2[36]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[38]) ;
+B0reg2 = _mm_load_pd(&B0[38]) ;
+B1reg2 = _mm_load_pd(&B1[38]) ;
+B2reg2 = _mm_load_pd(&B2[38]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[40]) ;
+B0reg1 = _mm_load_pd(&B0[40]) ;
+B1reg1 = _mm_load_pd(&B1[40]) ;
+B2reg1 = _mm_load_pd(&B2[40]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[42]) ;
+B0reg2 = _mm_load_pd(&B0[42]) ;
+B1reg2 = _mm_load_pd(&B1[42]) ;
+B2reg2 = _mm_load_pd(&B2[42]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[44]) ;
+B0reg1 = _mm_load_pd(&B0[44]) ;
+B1reg1 = _mm_load_pd(&B1[44]) ;
+B2reg1 = _mm_load_pd(&B2[44]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[46]) ;
+B0reg2 = _mm_load_pd(&B0[46]) ;
+B1reg2 = _mm_load_pd(&B1[46]) ;
+B2reg2 = _mm_load_pd(&B2[46]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[48]) ;
+B0reg1 = _mm_load_pd(&B0[48]) ;
+B1reg1 = _mm_load_pd(&B1[48]) ;
+B2reg1 = _mm_load_pd(&B2[48]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[50]) ;
+B0reg2 = _mm_load_pd(&B0[50]) ;
+B1reg2 = _mm_load_pd(&B1[50]) ;
+B2reg2 = _mm_load_pd(&B2[50]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_pd(&A[52]) ;
+B0reg1 = _mm_load_pd(&B0[52]) ;
+B1reg1 = _mm_load_pd(&B1[52]) ;
+B2reg1 = _mm_load_pd(&B2[52]) ;
+B0reg1 = _mm_mul_pd(B0reg1,Areg1) ;
+T0reg1 = _mm_add_pd(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_pd(B1reg1,Areg1) ;
+T1reg1 = _mm_add_pd(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_pd(B2reg1,Areg1) ;
+T2reg1 = _mm_add_pd(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_pd(&A[54]) ;
+B0reg2 = _mm_load_pd(&B0[54]) ;
+B1reg2 = _mm_load_pd(&B1[54]) ;
+B2reg2 = _mm_load_pd(&B2[54]) ;
+B0reg2 = _mm_mul_pd(B0reg2,Areg2) ;
+T0reg2 = _mm_add_pd(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_pd(B1reg2,Areg2) ;
+T1reg2 = _mm_add_pd(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_pd(B2reg2,Areg2) ;
+T2reg2 = _mm_add_pd(T2reg2,B2reg2) ;
+
+
+T0reg1 = _mm_add_pd(T0reg1,T0reg2) ;
+T1reg1 = _mm_add_pd(T1reg1,T1reg2) ;
+T2reg1 = _mm_add_pd(T2reg1,T2reg2) ;
+
+T0reg1 = _mm_hadd_pd(T0reg1,T0reg1) ;
+_mm_store_sd(tout0,T0reg1) ;
+T1reg1 = _mm_hadd_pd(T1reg1,T1reg1) ;
+_mm_store_sd(tout1,T1reg1) ;
+T2reg1 = _mm_hadd_pd(T2reg1,T2reg1) ;
+_mm_store_sd(tout2,T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_7042.c.h b/src/USER-MGPT/mgpt_ttr_7042.c.h
new file mode 100644
index 000000000..36ffe6714
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_7042.c.h
@@ -0,0 +1,194 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#include <xmmintrin.h>
+
+#include <pmmintrin.h>
+
+void ttr_7_8_3_v4r2(const float * restrict A,
+ const float * restrict B0,float * restrict tout0,
+ const float * restrict B1,float * restrict tout1,
+ const float * restrict B2,float * restrict tout2) {
+__m128 Areg1,Areg2;
+__m128 B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2;
+__m128 T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2;
+
+Areg1 = _mm_load_ps(&A[0]) ;
+T0reg1 = _mm_load_ps(&B0[0]) ;
+T1reg1 = _mm_load_ps(&B1[0]) ;
+T2reg1 = _mm_load_ps(&B2[0]) ;
+T0reg1 = _mm_mul_ps(T0reg1,Areg1) ;
+T1reg1 = _mm_mul_ps(T1reg1,Areg1) ;
+T2reg1 = _mm_mul_ps(T2reg1,Areg1) ;
+
+Areg2 = _mm_load_ps(&A[4]) ;
+T0reg2 = _mm_load_ps(&B0[4]) ;
+T1reg2 = _mm_load_ps(&B1[4]) ;
+T2reg2 = _mm_load_ps(&B2[4]) ;
+T0reg2 = _mm_mul_ps(T0reg2,Areg2) ;
+T1reg2 = _mm_mul_ps(T1reg2,Areg2) ;
+T2reg2 = _mm_mul_ps(T2reg2,Areg2) ;
+
+Areg1 = _mm_load_ps(&A[8]) ;
+B0reg1 = _mm_load_ps(&B0[8]) ;
+B1reg1 = _mm_load_ps(&B1[8]) ;
+B2reg1 = _mm_load_ps(&B2[8]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[12]) ;
+B0reg2 = _mm_load_ps(&B0[12]) ;
+B1reg2 = _mm_load_ps(&B1[12]) ;
+B2reg2 = _mm_load_ps(&B2[12]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[16]) ;
+B0reg1 = _mm_load_ps(&B0[16]) ;
+B1reg1 = _mm_load_ps(&B1[16]) ;
+B2reg1 = _mm_load_ps(&B2[16]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[20]) ;
+B0reg2 = _mm_load_ps(&B0[20]) ;
+B1reg2 = _mm_load_ps(&B1[20]) ;
+B2reg2 = _mm_load_ps(&B2[20]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[24]) ;
+B0reg1 = _mm_load_ps(&B0[24]) ;
+B1reg1 = _mm_load_ps(&B1[24]) ;
+B2reg1 = _mm_load_ps(&B2[24]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[28]) ;
+B0reg2 = _mm_load_ps(&B0[28]) ;
+B1reg2 = _mm_load_ps(&B1[28]) ;
+B2reg2 = _mm_load_ps(&B2[28]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[32]) ;
+B0reg1 = _mm_load_ps(&B0[32]) ;
+B1reg1 = _mm_load_ps(&B1[32]) ;
+B2reg1 = _mm_load_ps(&B2[32]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[36]) ;
+B0reg2 = _mm_load_ps(&B0[36]) ;
+B1reg2 = _mm_load_ps(&B1[36]) ;
+B2reg2 = _mm_load_ps(&B2[36]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[40]) ;
+B0reg1 = _mm_load_ps(&B0[40]) ;
+B1reg1 = _mm_load_ps(&B1[40]) ;
+B2reg1 = _mm_load_ps(&B2[40]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[44]) ;
+B0reg2 = _mm_load_ps(&B0[44]) ;
+B1reg2 = _mm_load_ps(&B1[44]) ;
+B2reg2 = _mm_load_ps(&B2[44]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+Areg1 = _mm_load_ps(&A[48]) ;
+B0reg1 = _mm_load_ps(&B0[48]) ;
+B1reg1 = _mm_load_ps(&B1[48]) ;
+B2reg1 = _mm_load_ps(&B2[48]) ;
+B0reg1 = _mm_mul_ps(B0reg1,Areg1) ;
+T0reg1 = _mm_add_ps(T0reg1,B0reg1) ;
+B1reg1 = _mm_mul_ps(B1reg1,Areg1) ;
+T1reg1 = _mm_add_ps(T1reg1,B1reg1) ;
+B2reg1 = _mm_mul_ps(B2reg1,Areg1) ;
+T2reg1 = _mm_add_ps(T2reg1,B2reg1) ;
+
+Areg2 = _mm_load_ps(&A[52]) ;
+B0reg2 = _mm_load_ps(&B0[52]) ;
+B1reg2 = _mm_load_ps(&B1[52]) ;
+B2reg2 = _mm_load_ps(&B2[52]) ;
+B0reg2 = _mm_mul_ps(B0reg2,Areg2) ;
+T0reg2 = _mm_add_ps(T0reg2,B0reg2) ;
+B1reg2 = _mm_mul_ps(B1reg2,Areg2) ;
+T1reg2 = _mm_add_ps(T1reg2,B1reg2) ;
+B2reg2 = _mm_mul_ps(B2reg2,Areg2) ;
+T2reg2 = _mm_add_ps(T2reg2,B2reg2) ;
+
+
+T0reg1 = _mm_add_ps(T0reg1,T0reg2) ;
+T1reg1 = _mm_add_ps(T1reg1,T1reg2) ;
+T2reg1 = _mm_add_ps(T2reg1,T2reg2) ;
+
+T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ;
+T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ;
+_mm_store_ss(tout0,T0reg1) ;
+T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ;
+T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ;
+_mm_store_ss(tout1,T1reg1) ;
+T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ;
+T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ;
+_mm_store_ss(tout2,T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_7123.c.h b/src/USER-MGPT/mgpt_ttr_7123.c.h
new file mode 100644
index 000000000..39828ab48
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_7123.c.h
@@ -0,0 +1,349 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+
+//#define TESTING
+
+#ifdef TESTING
+
+typedef struct {
+ double x,y;
+} pair;
+
+
+#define CPLX pair
+
+static double my_creal(CPLX x) {
+ return ((double *) &x)[0];
+}
+static double my_cimag(CPLX x) {
+ return ((double *) &x)[1];
+}
+static CPLX my_lfpd(const double *p) {
+ return ((CPLX *) p)[0];
+}
+
+/*
+// Not needed for trace calculations.
+static void my_stfpd(double *p,CPLX x) {
+ ((CPLX *) p)[0] = x;
+}
+static CPLX my_fxsmul(CPLX x,double a) {
+ double y[2];
+ y[0] = a * my_creal(x);
+ y[1] = a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) {
+ double y[2];
+ y[0] = my_creal(t) + a * my_creal(x);
+ y[1] = my_cimag(t) + a * my_cimag(x);
+ return ((CPLX *) y)[0];
+}
+*/
+
+static CPLX my_fpmul(CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(y) * my_creal(x);
+ U.z[1] = my_cimag(y) * my_cimag(x);
+ return U.c;
+}
+static CPLX my_fpadd(CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(y) + my_creal(x);
+ U.z[1] = my_cimag(y) + my_cimag(x);
+ return U.c;
+}
+static CPLX my_fpmadd(CPLX t,CPLX x,CPLX y) {
+ union {
+ double z[2];
+ CPLX c;
+ } U;
+ U.z[0] = my_creal(t) + my_creal(y) * my_creal(x);
+ U.z[1] = my_cimag(t) + my_cimag(y) * my_cimag(x);
+ return U.c;
+}
+
+#define __creal my_creal
+#define __cimag my_cimag
+#define __lfpd my_lfpd
+#define __stfpd my_stfpd
+#define __fxsmul my_fxsmul
+#define __fxcpmadd my_fxcpmadd
+
+#define __fpadd my_fpadd
+#define __fpmul my_fpmul
+#define __fpmadd my_fpmadd
+
+#else
+
+#define CPLX double _Complex
+
+#endif
+
+void ttr_bg_7_8_3_v2r3(const double * restrict A,
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
+CPLX Areg1,Areg2,Areg3;
+CPLX B0reg1,B0reg2,B0reg3,B1reg1,B1reg2,B1reg3,B2reg1,B2reg2,B2reg3;
+CPLX T0reg1,T0reg2,T0reg3,T1reg1,T1reg2,T1reg3,T2reg1,T2reg2,T2reg3;
+
+Areg1 = __lfpd(&A[0]) ;
+B0reg1 = __lfpd(&B0[0]) ;
+B1reg1 = __lfpd(&B1[0]) ;
+B2reg1 = __lfpd(&B2[0]) ;
+T0reg1 = __fpmul(Areg1,B0reg1) ;
+T1reg1 = __fpmul(Areg1,B1reg1) ;
+T2reg1 = __fpmul(Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[2]) ;
+B0reg2 = __lfpd(&B0[2]) ;
+B1reg2 = __lfpd(&B1[2]) ;
+B2reg2 = __lfpd(&B2[2]) ;
+T0reg2 = __fpmul(Areg2,B0reg2) ;
+T1reg2 = __fpmul(Areg2,B1reg2) ;
+T2reg2 = __fpmul(Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[4]) ;
+B0reg3 = __lfpd(&B0[4]) ;
+B1reg3 = __lfpd(&B1[4]) ;
+B2reg3 = __lfpd(&B2[4]) ;
+T0reg3 = __fpmul(Areg3,B0reg3) ;
+T1reg3 = __fpmul(Areg3,B1reg3) ;
+T2reg3 = __fpmul(Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[6]) ;
+B0reg1 = __lfpd(&B0[6]) ;
+B1reg1 = __lfpd(&B1[6]) ;
+B2reg1 = __lfpd(&B2[6]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[8]) ;
+B0reg2 = __lfpd(&B0[8]) ;
+B1reg2 = __lfpd(&B1[8]) ;
+B2reg2 = __lfpd(&B2[8]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[10]) ;
+B0reg3 = __lfpd(&B0[10]) ;
+B1reg3 = __lfpd(&B1[10]) ;
+B2reg3 = __lfpd(&B2[10]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[12]) ;
+B0reg1 = __lfpd(&B0[12]) ;
+B1reg1 = __lfpd(&B1[12]) ;
+B2reg1 = __lfpd(&B2[12]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[14]) ;
+B0reg2 = __lfpd(&B0[14]) ;
+B1reg2 = __lfpd(&B1[14]) ;
+B2reg2 = __lfpd(&B2[14]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[16]) ;
+B0reg3 = __lfpd(&B0[16]) ;
+B1reg3 = __lfpd(&B1[16]) ;
+B2reg3 = __lfpd(&B2[16]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[18]) ;
+B0reg1 = __lfpd(&B0[18]) ;
+B1reg1 = __lfpd(&B1[18]) ;
+B2reg1 = __lfpd(&B2[18]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[20]) ;
+B0reg2 = __lfpd(&B0[20]) ;
+B1reg2 = __lfpd(&B1[20]) ;
+B2reg2 = __lfpd(&B2[20]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[22]) ;
+B0reg3 = __lfpd(&B0[22]) ;
+B1reg3 = __lfpd(&B1[22]) ;
+B2reg3 = __lfpd(&B2[22]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[24]) ;
+B0reg1 = __lfpd(&B0[24]) ;
+B1reg1 = __lfpd(&B1[24]) ;
+B2reg1 = __lfpd(&B2[24]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[26]) ;
+B0reg2 = __lfpd(&B0[26]) ;
+B1reg2 = __lfpd(&B1[26]) ;
+B2reg2 = __lfpd(&B2[26]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[28]) ;
+B0reg3 = __lfpd(&B0[28]) ;
+B1reg3 = __lfpd(&B1[28]) ;
+B2reg3 = __lfpd(&B2[28]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[30]) ;
+B0reg1 = __lfpd(&B0[30]) ;
+B1reg1 = __lfpd(&B1[30]) ;
+B2reg1 = __lfpd(&B2[30]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[32]) ;
+B0reg2 = __lfpd(&B0[32]) ;
+B1reg2 = __lfpd(&B1[32]) ;
+B2reg2 = __lfpd(&B2[32]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[34]) ;
+B0reg3 = __lfpd(&B0[34]) ;
+B1reg3 = __lfpd(&B1[34]) ;
+B2reg3 = __lfpd(&B2[34]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[36]) ;
+B0reg1 = __lfpd(&B0[36]) ;
+B1reg1 = __lfpd(&B1[36]) ;
+B2reg1 = __lfpd(&B2[36]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[38]) ;
+B0reg2 = __lfpd(&B0[38]) ;
+B1reg2 = __lfpd(&B1[38]) ;
+B2reg2 = __lfpd(&B2[38]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[40]) ;
+B0reg3 = __lfpd(&B0[40]) ;
+B1reg3 = __lfpd(&B1[40]) ;
+B2reg3 = __lfpd(&B2[40]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[42]) ;
+B0reg1 = __lfpd(&B0[42]) ;
+B1reg1 = __lfpd(&B1[42]) ;
+B2reg1 = __lfpd(&B2[42]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[44]) ;
+B0reg2 = __lfpd(&B0[44]) ;
+B1reg2 = __lfpd(&B1[44]) ;
+B2reg2 = __lfpd(&B2[44]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[46]) ;
+B0reg3 = __lfpd(&B0[46]) ;
+B1reg3 = __lfpd(&B1[46]) ;
+B2reg3 = __lfpd(&B2[46]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[48]) ;
+B0reg1 = __lfpd(&B0[48]) ;
+B1reg1 = __lfpd(&B1[48]) ;
+B2reg1 = __lfpd(&B2[48]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+Areg2 = __lfpd(&A[50]) ;
+B0reg2 = __lfpd(&B0[50]) ;
+B1reg2 = __lfpd(&B1[50]) ;
+B2reg2 = __lfpd(&B2[50]) ;
+T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ;
+T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ;
+T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ;
+
+Areg3 = __lfpd(&A[52]) ;
+B0reg3 = __lfpd(&B0[52]) ;
+B1reg3 = __lfpd(&B1[52]) ;
+B2reg3 = __lfpd(&B2[52]) ;
+T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ;
+T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ;
+T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ;
+
+Areg1 = __lfpd(&A[54]) ;
+B0reg1 = __lfpd(&B0[54]) ;
+B1reg1 = __lfpd(&B1[54]) ;
+B2reg1 = __lfpd(&B2[54]) ;
+T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ;
+T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ;
+T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ;
+
+
+T0reg1 = __fpadd(T0reg1,T0reg2) ;
+T1reg1 = __fpadd(T1reg1,T1reg2) ;
+T2reg1 = __fpadd(T2reg1,T2reg2) ;
+T0reg1 = __fpadd(T0reg1,T0reg3) ;
+T1reg1 = __fpadd(T1reg1,T1reg3) ;
+T2reg1 = __fpadd(T2reg1,T2reg3) ;
+
+*tout0 = __creal(T0reg1) + __cimag(T0reg1) ;
+*tout1 = __creal(T1reg1) + __cimag(T1reg1) ;
+*tout2 = __creal(T2reg1) + __cimag(T2reg1) ;
+
+}
diff --git a/src/USER-MGPT/mgpt_ttr_7141.c.h b/src/USER-MGPT/mgpt_ttr_7141.c.h
new file mode 100644
index 000000000..830942233
--- /dev/null
+++ b/src/USER-MGPT/mgpt_ttr_7141.c.h
@@ -0,0 +1,174 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ This file is part of the MGPT implementation. See further comments
+ in pair_mgpt.cpp and pair_mgpt.h.
+------------------------------------------------------------------------- */
+
+#define vector vector4double
+#define my_vec_add(a,b) vec_add(a,b)
+#define my_vec_mul(a,b) vec_mul(a,b)
+#define my_vec_fma(a,b,c) vec_madd(b,c,a)
+#define my_vec_ld(ptr) vec_lda(0,ptr)
+#define my_vec_sldw(x,y,n) vec_sldw(x,y,n)
+#define my_vec_sts(x,ptr) vec_sts(x,0,ptr)
+
+#define const
+#define real double
+
+void ttr_bg_7_8_3_v4r1(const real * restrict A,
+ const real * restrict B0,real * restrict tout0,
+ const real * restrict B1,real * restrict tout1,
+ const real * restrict B2,real * restrict tout2) {
+vector Areg1;
+vector B0reg1,B1reg1,B2reg1;
+vector T0reg1,T1reg1,T2reg1;
+
+Areg1 = my_vec_ld(&A[0]) ;
+B0reg1 = my_vec_ld(&B0[0]) ;
+B1reg1 = my_vec_ld(&B1[0]) ;
+B2reg1 = my_vec_ld(&B2[0]) ;
+T0reg1 = my_vec_mul(Areg1,B0reg1) ;
+T1reg1 = my_vec_mul(Areg1,B1reg1) ;
+T2reg1 = my_vec_mul(Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[4]) ;
+B0reg1 = my_vec_ld(&B0[4]) ;
+B1reg1 = my_vec_ld(&B1[4]) ;
+B2reg1 = my_vec_ld(&B2[4]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[8]) ;
+B0reg1 = my_vec_ld(&B0[8]) ;
+B1reg1 = my_vec_ld(&B1[8]) ;
+B2reg1 = my_vec_ld(&B2[8]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[12]) ;
+B0reg1 = my_vec_ld(&B0[12]) ;
+B1reg1 = my_vec_ld(&B1[12]) ;
+B2reg1 = my_vec_ld(&B2[12]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[16]) ;
+B0reg1 = my_vec_ld(&B0[16]) ;
+B1reg1 = my_vec_ld(&B1[16]) ;
+B2reg1 = my_vec_ld(&B2[16]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[20]) ;
+B0reg1 = my_vec_ld(&B0[20]) ;
+B1reg1 = my_vec_ld(&B1[20]) ;
+B2reg1 = my_vec_ld(&B2[20]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[24]) ;
+B0reg1 = my_vec_ld(&B0[24]) ;
+B1reg1 = my_vec_ld(&B1[24]) ;
+B2reg1 = my_vec_ld(&B2[24]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[28]) ;
+B0reg1 = my_vec_ld(&B0[28]) ;
+B1reg1 = my_vec_ld(&B1[28]) ;
+B2reg1 = my_vec_ld(&B2[28]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[32]) ;
+B0reg1 = my_vec_ld(&B0[32]) ;
+B1reg1 = my_vec_ld(&B1[32]) ;
+B2reg1 = my_vec_ld(&B2[32]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[36]) ;
+B0reg1 = my_vec_ld(&B0[36]) ;
+B1reg1 = my_vec_ld(&B1[36]) ;
+B2reg1 = my_vec_ld(&B2[36]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[40]) ;
+B0reg1 = my_vec_ld(&B0[40]) ;
+B1reg1 = my_vec_ld(&B1[40]) ;
+B2reg1 = my_vec_ld(&B2[40]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[44]) ;
+B0reg1 = my_vec_ld(&B0[44]) ;
+B1reg1 = my_vec_ld(&B1[44]) ;
+B2reg1 = my_vec_ld(&B2[44]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[48]) ;
+B0reg1 = my_vec_ld(&B0[48]) ;
+B1reg1 = my_vec_ld(&B1[48]) ;
+B2reg1 = my_vec_ld(&B2[48]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+Areg1 = my_vec_ld(&A[52]) ;
+B0reg1 = my_vec_ld(&B0[52]) ;
+B1reg1 = my_vec_ld(&B1[52]) ;
+B2reg1 = my_vec_ld(&B2[52]) ;
+T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ;
+T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ;
+T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ;
+
+
+
+T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,2));
+T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,1));
+my_vec_sts(T0reg1,tout0);
+T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,2));
+T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,1));
+my_vec_sts(T1reg1,tout1);
+T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,2));
+T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,1));
+my_vec_sts(T2reg1,tout2);
+
+}
+
+
+#undef vector
+#undef my_vec_add
+#undef my_vec_mul
+#undef my_vec_fma
+#undef my_vec_ld
+#undef my_vec_sldw
+#undef my_vec_sts
+
+#undef const
+#undef real
diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp
new file mode 100644
index 000000000..596e66f48
--- /dev/null
+++ b/src/USER-MGPT/pair_mgpt.cpp
@@ -0,0 +1,2927 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
+ and John Moriarty, LLNL (moriarty2@llnl.gov)
+
+ Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
+ matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted
+ to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski
+ (2011). See LLNL copyright notice at bottom of this file.
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cassert>
+
+#include "pair_mgpt.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "memory.h"
+#include "error.h"
+
+
+using namespace LAMMPS_NS;
+
+//#define TIMING_ON
+
+#ifdef TIMING_ON
+#include <sys/time.h>
+#include <time.h>
+//#include "rdtsc.h"
+#ifdef __bgq__
+#include <hwi/include/bqc/A2_inlines.h>
+#endif
+
+static double gettime(int x = 0) {
+ if(1) {
+ /*
+ struct timeval tv;
+ gettimeofday(&tv,NULL);
+ return tv.tv_sec + 1e-6 * tv.tv_usec;
+ */
+ /*
+ const double x = 1.0 / CLOCKS_PER_SEC;
+ return clock() * x;
+ */
+
+ //const double invfreq = 1.0 / 2394.108e6;
+ /*
+ const double invfreq = 1.0 / 700e6;
+ unsigned long long int x = rdtsc();
+ return x*invfreq;
+ */
+
+ const double invfreq = 1.0 / 1.6e9;
+ unsigned long long int x = GetTimeBase();
+ return x*invfreq;
+
+
+ } else
+ return 0.0;
+}
+#else
+static double gettime(int x = 0) { return 0.0; }
+#endif
+
+
+/* ---------------------------------------------------------------------- */
+
+PairMGPT::PairMGPT(LAMMPS *lmp) : Pair(lmp)
+{
+ single_enable = 0;
+ one_coeff = 1;
+ ghostneigh = 1;
+}
+
+PairMGPT::~PairMGPT()
+{
+ if(allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(cutghost);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+
+static double t_make_b2 = 0.0,n_make_b2 = 0.0;
+
+template<typename intype,typename outtype,int ni,int nj> void fmatconv(intype *array) {
+ outtype *cast = (outtype *) array;
+ for(int i = 0; i<ni; i++)
+ for(int j = 0; j<nj; j++)
+ cast[i*nj+j] = array[i*nj+j];
+}
+
+void PairMGPT::make_bond(const double xx[][3],int i,int j,bond_data *bptr) {
+ double rrij[3],rij;
+ int p;
+
+ double t0,t1;
+
+ /* Check that alignment requirements for SIMD code are fullfilled */
+ assert( (((unsigned long long int) (bptr->H.m )) & 31) == 0 );
+ assert( (((unsigned long long int) (bptr->Hx.m)) & 31) == 0 );
+ assert( (((unsigned long long int) (bptr->Hy.m)) & 31) == 0 );
+ assert( (((unsigned long long int) (bptr->Hz.m)) & 31) == 0 );
+
+ rij = 0.0;
+ for(p = 0; p<3; p++) {
+ rrij[p] = xx[i][p] - xx[j][p];
+ rij = rij + rrij[p]*rrij[p];
+ }
+
+ /* Zero all matrix elements */
+ for(i = 0; i<8; i++)
+ for(j = 0; j<8; j++) {
+ bptr->H.m[i][j] = 0.0;
+ bptr->Hx.m[i][j] = 0.0;
+ bptr->Hy.m[i][j] = 0.0;
+ bptr->Hz.m[i][j] = 0.0;
+ bptr->Hz.m[j][i] = 0.0;
+ }
+
+ if(rij <= rcrit*rcrit) {
+ t0 = gettime();
+ if(lang == 3) {
+ hamltn_5_raw(rrij[0],rrij[1],rrij[2],
+ bptr->H.m ,bptr->Hx.m,
+ bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum);
+ } else {
+ hamltn_7_raw(rrij[0],rrij[1],rrij[2],
+ bptr->H.m ,bptr->Hx.m,
+ bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum);
+ }
+
+ t1 = gettime();
+ t_make_b2 += t1-t0;
+ n_make_b2++;
+ } else {
+ bptr->fl_deriv_sum = 0.0;
+ }
+
+ if(linalg.single) {
+ fmatconv<double,float,7,8>(&(bptr->H.m[1][0]));
+ fmatconv<double,float,7,8>(&(bptr->Hx.m[1][0]));
+ fmatconv<double,float,7,8>(&(bptr->Hy.m[1][0]));
+ fmatconv<double,float,7,8>(&(bptr->Hz.m[1][0]));
+ }
+}
+
+static double t_trace = 0.0,n_trace = 0.0;
+/*
+static inline double mtrace(int n,double A[8][8],double B[8][8]) {
+ double t0,t1;
+ double s;
+
+ t0 = gettime();
+ if(n == 5) s = mtrace_5(A,B);
+ else if(n == 7) s = mtrace_7(A,B);
+ else {
+ s = 0.0;
+ for(int i = 1; i<=n; i++)
+ for(int j = 1; j<=n; j++)
+ s = s + A[i][j]*B[i][j];
+ }
+ t1 = gettime();
+ t_trace += t1-t0;
+ n_trace++;
+
+ return s;
+}
+*/
+
+void PairMGPT::make_triplet(bond_data *ij_bond,bond_data *ik_bond,
+ triplet_data *triptr) {
+ if(1) {
+ const trmul_fun tr_mul = linalg.tr_mul;
+ tr_mul(&(ij_bond->H.m[1][0]), &(ik_bond->H.m[1][0]) ,&(triptr->H1H2.m[1][0]) );
+ tr_mul(&(ij_bond->Hx.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1xH2.m[1][0]));
+ tr_mul(&(ij_bond->Hy.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1yH2.m[1][0]));
+ tr_mul(&(ij_bond->Hz.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1zH2.m[1][0]));
+ tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hx.m[1][0]),&(triptr->H1H2x.m[1][0]));
+ tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hy.m[1][0]),&(triptr->H1H2y.m[1][0]));
+ tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hz.m[1][0]),&(triptr->H1H2z.m[1][0]));
+ } else {
+ transprod(ij_bond->H, ik_bond->H ,triptr->H1H2 );
+ transprod(ij_bond->Hx,ik_bond->H ,triptr->H1xH2);
+ transprod(ij_bond->Hy,ik_bond->H ,triptr->H1yH2);
+ transprod(ij_bond->Hz,ik_bond->H ,triptr->H1zH2);
+ transprod(ij_bond->H ,ik_bond->Hx,triptr->H1H2x);
+ transprod(ij_bond->H ,ik_bond->Hy,triptr->H1H2y);
+ transprod(ij_bond->H ,ik_bond->Hz,triptr->H1H2z);
+ }
+}
+
+static double t_make_t = 0.0,t_make_b = 0.0,n_make = 0.0;
+
+PairMGPT::triplet_data *PairMGPT::get_triplet(const double xx[][3],int i,int j,int k,
+ Hash<bond_data,Doublet> *bhash,
+ triplet_data *twork,
+ double *dvir_ij_p,double *dvir_ik_p) {
+ const int recompute = 0;
+ static bond_data bij_work,bik_work;
+
+ double t0,t1;
+
+ bond_data *bij = 0,*bik = 0;
+ triplet_data *tptr = 0;
+
+ t0 = gettime();
+ if(recompute == 0) {
+ bij = bhash->Lookup(Doublet(i,j));
+ bik = bhash->Lookup(Doublet(i,k));
+ }
+
+ if(bij == 0) {
+ if(recompute == 0)
+ bij = bhash->Insert(Doublet(i,j));
+ else
+ bij = &bij_work;
+ if(i < j)
+ make_bond(xx,i,j,bij);
+ else
+ make_bond(xx,j,i,bij);
+ }
+
+ if(bik == 0) {
+ if(recompute == 0)
+ bik = bhash->Insert(Doublet(i,k));
+ else
+ bik = &bik_work;
+ if(i < k)
+ make_bond(xx,i,k,bik);
+ else
+ make_bond(xx,k,i,bik);
+ }
+ t1 = gettime();
+ t_make_b += t1-t0;
+
+ t0 = gettime();
+ if(bij != 0 && bij != 0) {
+ tptr = twork;
+ make_triplet(bij,bik,tptr);
+ *dvir_ij_p = bij->fl_deriv_sum;
+ *dvir_ik_p = bik->fl_deriv_sum;
+ } else {
+ *dvir_ij_p = 0.0;
+ *dvir_ik_p = 0.0;
+ }
+ t1 = gettime();
+ t_make_t += t1-t0;
+ n_make++;
+ return tptr;
+}
+
+
+double PairMGPT::numderiv3t(double xx[][3],int i,int j,int k,int p) {
+ static bond_data Bij,Bjk,Bki;
+ const double delta = 1e-5;
+
+ const double xsave = xx[i][p];
+ double e1,e2;
+
+ const double vc = splinepot.vc;
+
+ xx[i][p] = xsave + delta;
+ make_bond(xx,i,j,&Bij);
+ make_bond(xx,j,k,&Bjk);
+ make_bond(xx,k,i,&Bki);
+ e1 = trace(prodmat(Bij.H,Bjk.H),Bki.H) * (vc/anorm3);
+
+ xx[i][p] = xsave - delta;
+ make_bond(xx,i,j,&Bij);
+ if(0) { /* This bond doesn't change when i is perturbed */
+ make_bond(xx,j,k,&Bjk);
+ }
+ make_bond(xx,k,i,&Bki);
+ e2 = trace(prodmat(Bij.H,Bjk.H),Bki.H) * (vc/anorm3);
+
+ xx[i][p] = xsave;
+ return (e1 - e2)/(2.0*delta);
+}
+
+double PairMGPT::numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert) {
+ static bond_data Bij,Bik;
+ const double delta = 1e-5;
+
+ const double xsave = xx[ipert][p];
+ double e1,e2;
+
+ const double vd = splinepot.vd;
+
+ xx[ipert][p] = xsave + delta;
+ make_bond(xx,i,j,&Bij);
+ make_bond(xx,i,k,&Bik);
+ e1 = trace(prodmat(Bij.H,Bij.H),prodmat(Bik.H,Bik.H)) * (vd/anorm4);
+
+ xx[ipert][p] = xsave - delta;
+ make_bond(xx,i,j,&Bij);
+ make_bond(xx,i,k,&Bik);
+ e2 = trace(prodmat(Bij.H,Bij.H),prodmat(Bik.H,Bik.H)) * (vd/anorm4);
+
+ xx[ipert][p] = xsave;
+ return (e1 - e2)/(2.0*delta);
+}
+
+
+double PairMGPT::numderiv4(double xx[][3],int i,int j,int k,int m,int p) {
+ static bond_data Bij,Bjk,Bkm,Bmi;
+ const double delta = 1e-5;
+
+ const double xsave = xx[i][p];
+ double e1,e2;
+
+ const double ve = splinepot.ve;
+
+ xx[i][p] = xsave + delta;
+ make_bond(xx,i,j,&Bij);
+ make_bond(xx,j,k,&Bjk);
+ make_bond(xx,k,m,&Bkm);
+ make_bond(xx,m,i,&Bmi);
+ e1 = trace(prodmat(Bij.H,Bjk.H),prodmat(Bkm.H,Bmi.H)) * (ve/anorm4);
+
+ xx[i][p] = xsave - delta;
+ make_bond(xx,i,j,&Bij);
+ if(0) { /* Only the i coordinates changed... */
+ make_bond(xx,j,k,&Bjk);
+ make_bond(xx,k,m,&Bkm);
+ }
+ make_bond(xx,m,i,&Bmi);
+ e2 = trace(prodmat(Bij.H,Bjk.H),prodmat(Bkm.H,Bmi.H)) * (ve/anorm4);
+
+ xx[i][p] = xsave;
+ return (e1 - e2)/(2.0*delta);
+}
+
+static double dtol = 1e-6;
+void PairMGPT::force_debug_3t(double xx[][3],
+ int i0,int j0,int k0,
+ int i ,int j ,int k ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz) {
+ double dfi[3],dfj[3],dfk[3];
+ dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz;
+ dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
+ dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
+
+ for(int p = 0; p<3; p++) {
+ /* Compute numerical derivatives by displacing atoms i,j,k */
+ double ndfi,ndfj,ndfk;
+ ndfi = -numderiv3t(xx,i,j,k,p);
+ ndfj = -numderiv3t(xx,j,k,i,p);
+ ndfk = -numderiv3t(xx,k,i,j,p);
+
+ if((fabs(dfi[p] - ndfi) > dtol &&
+ fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) ||
+ (fabs(dfj[p] - ndfj) > dtol &&
+ fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) ||
+ (fabs(dfk[p] - ndfk) > dtol &&
+ fabs(dfk[p] - ndfk) > dtol*fabs(ndfk))) {
+ printf("Force error in T12 & T23 & T31 :: i,j,k = %d,%d,%d\n",i0,j0,k0);
+ printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
+ printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf("\n");
+ }
+ }
+}
+
+void PairMGPT::force_debug_3v(double xx[][3],
+ int i0,int j0,int k0,
+ int i ,int j ,int k ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz) {
+ double dfi[3],dfj[3],dfk[3];
+ dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz;
+ dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
+ dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
+
+ for(int p = 0; p<3; p++) {
+ /* Compute numerical derivatives by displacing atoms i,j,k */
+ double ndfi,ndfj,ndfk;
+ ndfi = -numderiv3v(xx,i,j,k,p,i0);
+ ndfj = -numderiv3v(xx,i,j,k,p,j0);
+ ndfk = -numderiv3v(xx,i,j,k,p,k0);
+
+ if((fabs(dfi[p] - ndfi) > dtol &&
+ fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) ||
+ (fabs(dfj[p] - ndfj) > dtol &&
+ fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) ||
+ (fabs(dfk[p] - ndfk) > dtol &&
+ fabs(dfk[p] - ndfk) > dtol*fabs(ndfk))) {
+ printf("Force error in T12 :: i,j,k = %d,%d,%d\n",i0,j0,k0);
+ printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
+ printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf("\n");
+ }
+ }
+}
+
+void PairMGPT::force_debug_4(double xx[][3],
+ int i0,int j0,int k0,int m0,
+ int i ,int j ,int k ,int m ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz,
+ double dfmx,double dfmy,double dfmz) {
+
+ double dfi[3],dfj[3],dfk[3],dfm[3];
+ dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz;
+ dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
+ dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
+ dfm[0] = dfmx; dfm[1] = dfmy; dfm[2] = dfmz;
+
+ const int ii0[] = {i0,j0,k0,m0},ii[] = {i,j,k,m,i,j,k};
+
+ for(int p = 0; p<3; p++) {
+ /* Compute numerical derivatives by displacing atoms i,j,k,m */
+ double ndfi,ndfj,ndfk,ndfm;
+ if(1) {
+ double ndf[] = {0.0,0.0,0.0,0.0};
+ for(int s = 0; s<4; s++)
+ for(int t = 0; t<4; t++)
+ if(ii[s] == ii0[t])
+ ndf[t] = -numderiv4(xx,ii[s],ii[s+1],ii[s+2],ii[s+3],p);
+ ndfi = ndf[0]; ndfj = ndf[1];
+ ndfk = ndf[2]; ndfm = ndf[3];
+ } else {
+ ndfi = -numderiv4(xx,i,j,k,m,p);
+ ndfj = -numderiv4(xx,j,k,m,i,p);
+ ndfk = -numderiv4(xx,k,m,i,j,p);
+ ndfm = -numderiv4(xx,m,i,j,k,p);
+ }
+
+ if((fabs(dfi[p] - ndfi) > dtol &&
+ fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) ||
+ (fabs(dfj[p] - ndfj) > dtol &&
+ fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) ||
+ (fabs(dfk[p] - ndfk) > dtol &&
+ fabs(dfk[p] - ndfk) > dtol*fabs(ndfk)) ||
+ (fabs(dfm[p] - ndfm) > dtol &&
+ fabs(dfm[p] - ndfm) > dtol*fabs(ndfm))) {
+ printf("Force error in T31 & T64 :: i,j,k,m = %d,%d,%d,%d\n",i0,j0,k0,m0);
+ printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
+ printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf(" dE/d%c[m] = %20.10e %20.10e\n", 'x'+p,ndfm, dfm[p]);
+ printf("\n");
+ }
+ }
+}
+
+
+
+/*
+#define trd_update_4(T12,T45,coord) \
+ do { \
+ trd1 = transtrace(T12->H1##coord##H2,T45->H1H2 ); \
+ trd2 = transtrace(T12->H1H2##coord,T45->H1H2 ); \
+ trd3 = transtrace(T12->H1H2 ,T45->H1##coord##H2); \
+ trd4 = transtrace(T12->H1H2 ,T45->H1H2##coord ); \
+ } while(0)
+*/
+#define trd_update_4(T12,T45) \
+ do { \
+ tr_trace3(&(T45->H1H2.m[1][0]), \
+ &(T12->H1xH2.m[1][0]),&utr1x.d, \
+ &(T12->H1yH2.m[1][0]),&utr1y.d, \
+ &(T12->H1zH2.m[1][0]),&utr1z.d); \
+ tr_trace3(&(T45->H1H2.m[1][0]), \
+ &(T12->H1H2x.m[1][0]),&utr2x.d, \
+ &(T12->H1H2y.m[1][0]),&utr2y.d, \
+ &(T12->H1H2z.m[1][0]),&utr2z.d); \
+ tr_trace3(&(T12->H1H2.m[1][0]), \
+ &(T45->H1xH2.m[1][0]),&utr3x.d, \
+ &(T45->H1yH2.m[1][0]),&utr3y.d, \
+ &(T45->H1zH2.m[1][0]),&utr3z.d); \
+ tr_trace3(&(T12->H1H2.m[1][0]), \
+ &(T45->H1H2x.m[1][0]),&utr4x.d, \
+ &(T45->H1H2y.m[1][0]),&utr4y.d, \
+ &(T45->H1H2z.m[1][0]),&utr4z.d); \
+ if(linalg.single) { \
+ trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f; trd4x = utr4x.f; \
+ trd1y = utr1y.f; trd2y = utr2y.f; trd3y = utr3y.f; trd4y = utr4y.f; \
+ trd1z = utr1z.f; trd2z = utr2z.f; trd3z = utr3z.f; trd4z = utr4z.f; \
+ } else { \
+ trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d; trd4x = utr4x.d; \
+ trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d; trd4y = utr4y.d; \
+ trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d; trd4z = utr4z.d; \
+ } \
+ } while(0)
+
+#define dfix_update_4a(coord) \
+ do { \
+ dfi##coord = ( (-sij)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \
+ dfj##coord = ( ( sij)*trd1##coord + (-sjk)*trd2##coord ) * (ve / anorm4); \
+ dfk##coord = ( ( sjk)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \
+ dfm##coord = ( ( sim)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \
+ } while(0)
+
+
+#define dfix_update_4b(coord) \
+ do { \
+ dfi##coord = ( ( ski)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \
+ dfj##coord = ( (-sjk)*trd2##coord + (-sjm)*trd4##coord ) * (ve / anorm4); \
+ dfk##coord = ( (-ski)*trd1##coord + ( sjk)*trd2##coord ) * (ve / anorm4); \
+ dfm##coord = ( ( sim)*trd3##coord + ( sjm)*trd4##coord ) * (ve / anorm4); \
+ } while(0);
+
+#define dfix_update_4c(coord) \
+ do { \
+ dfi##coord = ( (-sij)*trd1##coord + ( ski)*trd2##coord ) * (ve / anorm4); \
+ dfj##coord = ( ( sij)*trd1##coord + (-sjm)*trd3##coord ) * (ve / anorm4); \
+ dfk##coord = ( (-ski)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \
+ dfm##coord = ( ( sjm)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \
+ } while(0);
+
+#define accumulate_forces_2(w) \
+ do { \
+ fix = fix + dfix*(w); \
+ fiy = fiy + dfiy*(w); \
+ fiz = fiz + dfiz*(w); \
+ \
+ fjx = fjx + dfjx*(w); \
+ fjy = fjy + dfjy*(w); \
+ fjz = fjz + dfjz*(w); \
+ } while(0)
+
+#define accumulate_forces_3(w) \
+ do { \
+ accumulate_forces_2(w); \
+ fkx = fkx + dfkx*(w); \
+ fky = fky + dfky*(w); \
+ fkz = fkz + dfkz*(w); \
+ } while(0)
+
+#define accumulate_forces_4(w) \
+ do { \
+ accumulate_forces_3(w); \
+ fmx = fmx + dfmx*(w); \
+ fmy = fmy + dfmy*(w); \
+ fmz = fmz + dfmz*(w); \
+ } while(0)
+
+
+
+#define restrict __restrict__
+#ifdef __bg__
+#define const
+#endif
+static int ntr_calls = 0;
+static trtrace3_fun tr_internal;
+static void tr_count(const double * restrict A,
+ const double * restrict B1,double * restrict t1,
+ const double * restrict B2,double * restrict t2,
+ const double * restrict B3,double * restrict t3) {
+ tr_internal(A,B1,t1,B2,t2,B3,t3);
+ ntr_calls++;
+}
+#ifdef __bg__
+#undef const
+#endif
+#undef restrict
+
+
+int PairMGPT::Matrix::sz;
+void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
+ double *e_s,double *e_p,double *e_t,double *e_q,
+ int evflag,int newton_pair) {
+ Hash<bond_data,Doublet> bond_hash(100000);
+ int i,j,k,m,ix,jx,kx,mx,itag,jtag,p;
+
+ double e_single,e_pair,e_triplet,e_triplet_c,e_quad;
+ double volvir2;
+
+ double nbc = 0.0,tbl = 0.0,tbm = 0.0;
+ const int lmax_local = lmax;
+
+ //if(evflag) printf("##### ev flag is set... wasting cycles...\n");
+
+ *e_s = -99.0;
+ *e_p = -99.0;
+ *e_t = -99.0;
+ *e_q = -99.0;
+
+ double t0,t1;
+
+ t0 = gettime(1);
+ e_single = e_pair = e_triplet = e_triplet_c = e_quad = 0.0;
+ volvir2 = 0.0;
+
+ t_make_t = t_make_b = t_make_b2 = t_trace = 0.0;
+ n_make = n_make_b2 = n_trace = 0.0;
+
+ double tx0,tx1,tsort = 0.0,tpair = 0.0,tlookup = 0.0;
+ double ttriplet = 0.0,tquad = 0.0,tmem = 0.0;
+ double ntsort = 0.0,ntpair = 0.0,ntlookup = 0.0;
+ double nttriplet = 0.0,ntquad = 0.0,ntmem = 0.0,ntquaditer = 0.0;
+ double mcount = 0.0,mcount2 = 0.0, qcount = 0.0;
+
+ double fix,fjx,fkx,fmx,dfix,dfjx,dfkx,dfmx;
+ double fiy,fjy,fky,fmy,dfiy,dfjy,dfky,dfmy;
+ double fiz,fjz,fkz,fmz,dfiz,dfjz,dfkz,dfmz;
+
+ double fsave[4][3] = { {0.0} } /* {{0.0}} is to get rid of uninitialized use warning */;
+
+ //const int numerical_pair_forces = (nbody_flag/16)%2;
+ const int pair_forces = (nbody_flag/2)%2,three_body_forces = (nbody_flag/4)%2,four_body_forces = (nbody_flag/8)%2;
+ const int pair_energies = (nbody_flag/2)%2,three_body_energies = (nbody_flag/4)%2,four_body_energies = (nbody_flag/8)%2;
+ const int single_energies = nbody_flag%2;
+
+ const int triplet_debug = 0,quad_debug = 0;
+
+ /* Energy and force scale factor for unit conversion. */
+ const double e_scale = 0.5;
+
+#ifdef NEIGHMASK
+#define NIDX(x) (x)
+#else
+#define NIDX(x) ((x) & NEIGHMASK)
+#endif
+
+ int nneitot,*first,*nlist_short;
+ double w2,w3,w4;
+ triplet_data T12work,T23work,T31work,T45work,T56work,T64work;
+ triplet_data *T12,*T23,*T31,*T45,*T56,*T64;
+ int c_ij,c_jk,c_ki,c_im,c_jm,c_km;
+ int mi,mj,mk;
+ double tr0,tr1,tr2,tr3;
+ double v33,v43;
+ double rcut2_pair = rmax*rmax,rcut2_bond = rcrit*rcrit,rij2;
+ int ntot,nloc;
+
+ double dvir_ij,dvir_jk,dvir_ki,dvir_im,dvir_jm,dvir_km;
+ double vir3t = 0.0,vir3v = 0.0,vir4 = 0.0;
+
+ double (*xx)[3],(*ff)[3],(*ss)[3];
+
+#ifdef TIMING_ON
+ tr_internal = linalg.tr_trace; ntr_calls = 0;
+ const trtrace3_fun tr_trace3 = tr_count;
+#else
+ const trtrace3_fun tr_trace3 = linalg.tr_trace;
+#endif
+ union {
+ double d;
+ float f;
+ } utr1x,utr2x,utr3x,utr4x,utr1y,utr2y,utr3y,utr4y,utr1z,utr2z,utr3z,utr4z;
+ double trd1x,trd2x,trd3x,trd4x;
+ double trd1y,trd2y,trd3y,trd4y;
+ double trd1z,trd2z,trd3z,trd4z;
+
+
+ tx0 = gettime();
+
+ double rhoinv;
+ {
+ double vtot = 1.0;
+ double ntot = atom->natoms;
+ for(i = 0; i<3; i++)
+ vtot = vtot * (domain->boxhi[i] - domain->boxlo[i]);
+ rhoinv = vtot / ntot;
+ }
+
+ /* Make sure triplet data work area is aligned and zeroed out. */ {
+ assert(T12work.align_check() == 0);
+ assert(T23work.align_check() == 0);
+ assert(T31work.align_check() == 0);
+ assert(T45work.align_check() == 0);
+ assert(T56work.align_check() == 0);
+ assert(T64work.align_check() == 0);
+
+ T12work.zero(); T23work.zero(); T31work.zero();
+ T45work.zero(); T56work.zero(); T64work.zero();
+ }
+
+ ntot = atom->nlocal + atom->nghost;
+ nloc = atom->nlocal;
+ //printf("[%3d] Allocating local array, size is %d atoms...\n",comm->me,j);
+ xx = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,"mgpt: local position vector.");
+ ff = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,"mgpt: local force vector.");
+ //printf("[%3d] Initializing arrays...\n",comm->me);
+
+ const int triclinic = domain->triclinic;
+ double alpha[3] = {0.0,0.0,0.0};
+ if(triclinic) {
+ double E[3][3],EX[3][3];
+ int cyc[] = {0,1,2,0,1};
+
+ ss = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,
+ "mgpt: local reduced coordinate vector.");
+
+ for(i = 0; i<3; i++) {
+ for(j = 0; j<3; j++)
+ E[i][j] = 0.0;
+ E[i][i] = domain->subhi_lamda[i] - domain->sublo_lamda[i];
+ domain->lamda2x(E[i],EX[i]);
+ }
+ for(i = 0; i<3; i++) {
+ int i1 = cyc[i+1],i2 = cyc[i+2];
+ double dot = 0.0,ns2 = 0.0;
+ for(j = 0; j<3; j++) {
+ int j1 = cyc[j+1],j2 = cyc[j+2];
+ double cj = EX[i1][j1]*EX[i2][j2] - EX[i1][j2]*EX[i2][j1];
+ ns2 = ns2 + cj*cj;
+ dot = dot + EX[i][j]*cj;
+ }
+ alpha[i] = E[i][i] / (dot/sqrt(ns2));
+ if(comm->me == 0) {
+ static int count = 0;
+ if(count < 3)
+ printf("@@@ alpha(%d) = %15.5e\n",i+1,alpha[i]);
+ count++;
+ }
+ if(alpha[i] < 0.0) alpha[i] = -alpha[i];
+ }
+ } else
+ ss = xx;
+
+ nneitot = 0;
+ for(ix = 0; ix<ntot; ix++) {
+ for(p = 0; p<3; p++) {
+ xx[ix][p] = atom->x[ix][p];
+ ff[ix][p] = 0.0;
+ }
+ if(triclinic)
+ domain->x2lamda(xx[ix],ss[ix]);
+ nneitot = nneitot + nnei[ix];
+ }
+
+ first = (int *) memory->smalloc(sizeof(int) * (ntot+1),"mgpt: first");
+ nlist_short = (int *) memory->smalloc(sizeof(int) * nneitot,"mgpt: nlist_short");
+
+ tx1 = gettime();
+ tmem += tx1-tx0;
+ ntmem++;
+
+ //printf("[%3d] Starting calculation...\n",comm->me);
+
+
+ fix = fjx = fkx = fmx = 0.0;
+ fiy = fjy = fky = fmy = 0.0;
+ fiz = fjz = fkz = fmz = 0.0;
+
+ int c_p = 0, c_t = 0, c_q = 0;
+
+ if(0)
+ if(domain->triclinic) {
+ if(comm->me == 0)
+ printf("Can not handle triclinic box yet\n");
+ error->all(__FILE__,__LINE__,"Can not handle triclinic cell with mgpt yet.");
+ }
+
+ /*
+ for(i = 0; i<nloc; i++) {
+ printf("Atom %3d:: %10.3f %10.3f %10.3f\n",
+ i,xx[i][0],xx[i][1],xx[i][2]);
+ }
+ */
+
+ first[0] = 0;
+ for(i = 0; i<ntot; i++) {
+ fix = fiy = fiz = 0.0;
+
+ first[i+1] = first[i];
+
+ const int c1 = c1_outside(ss[i],triclinic,alpha);
+
+ tx0 = gettime();
+ for(jx = 0; jx<nnei[i]; jx++) {
+ fjx = fjy = fjz = 0.0;
+
+ j = NIDX( nlist[i][jx] );
+
+ rij2 = 0.0;
+ for(p = 0; p<3; p++) {
+ double t = xx[i][p] - xx[j][p];
+ rij2 = rij2 + t*t;
+ }
+
+ if(c1 == 0 && rij2 < rcut2_pair) {
+ if(j < i) {
+ w2 = get_weight(triclinic,ss[i],ss[j]);
+
+ if(w2 > 0.0) {
+ /*
+ Compute pair energy/force
+ */
+ double de_pair,df,rij = sqrt(rij2);
+ splinepot.eval_pot(rij,&de_pair,&df);
+ de_pair = de_pair * e_scale * w2;
+ df = df / rij * w2;
+
+
+ if(pair_energies == 0) de_pair = 0.0;
+ e_pair = e_pair + de_pair;
+ c_p++;
+
+ if(pair_forces == 0) df = 0.0;
+
+ if(volpres_flag && pair_energies) {
+ double dvir;
+ splinepot.eval_vir(rij,&dvir);
+ volvir2 = volvir2 - dvir * w2;
+
+ /* Per-atom virial contribution of volumetric energy term */
+ if(vflag_atom)
+ for(int pp = 0; pp<3; pp++) {
+ //virial[i] = virial[i] + rhoinv*e_scale*volvir2;
+ vatom[i][pp] -= 0.5 * rhoinv*e_scale*dvir*w2;
+ vatom[j][pp] -= 0.5 * rhoinv*e_scale*dvir*w2;
+ }
+ }
+
+ double drijx = xx[j][0] - xx[i][0];
+ double drijy = xx[j][1] - xx[i][1];
+ double drijz = xx[j][2] - xx[i][2];
+
+ fix = fix + df*drijx;
+ fjx = fjx - df*drijx;
+
+ fiy = fiy + df*drijy;
+ fjy = fjy - df*drijy;
+
+ fiz = fiz + df*drijz;
+ fjz = fjz - df*drijz;
+
+ if(evflag) {
+ //ev_tally(i,j,nloc,newton_pair,de_pair,0.0,df,-drijx,-drijy,-drijz);
+ /* To fix stress-per-atom scaling, and sign */
+ ev_tally(i,j,nloc,newton_pair,de_pair,0.0,-df * e_scale,-drijx,-drijy,-drijz);
+ }
+
+ ff[j][0] += fjx * e_scale;
+ ff[j][1] += fjy * e_scale;
+ ff[j][2] += fjz * e_scale;
+
+ }
+ }
+ }
+
+ if(rij2 < rcut2_bond && c2_outside(ss[i],ss[j],triclinic,alpha) == 0) {
+ /*
+ Add j to short neighbor list for i.
+ Insert j to keep list sorted.
+ */
+
+ p = first[i+1]-1;
+ while(p >= first[i] && nlist_short[p] > j) {
+ nlist_short[p+1] = nlist_short[p];
+ p = p - 1;
+ }
+ nlist_short[p+1] = j;
+ first[i+1] = first[i+1] + 1;
+ if(first[i+1] > nneitot) {
+ printf("nneitot = %d, short list full. i=%d\n",
+ nneitot,i);
+ error->one(__FILE__,__LINE__,"Shit! Short list full\n");
+ }
+
+ }
+ }
+
+ ff[i][0] += fix * e_scale;
+ ff[i][1] += fiy * e_scale;
+ ff[i][2] += fiz * e_scale;
+
+ tx1 = gettime();
+ tpair += tx1-tx0;
+ ntpair += nnei[i];
+ }
+
+ for(i = 0; i<ntot; i++) {
+ fix = fiy = fiz = 0.0;
+
+ /*
+ Use short lists for triplets and quadruplets.
+ For open (2-bonded) triplets, can only use k<j, but not k<i.
+ For closed (3-bonded) triplets, we can assume k<j<i.
+
+ Quadruplets:
+ Always use k<j<i, and require m<i.
+ If 5-bonded with im bond, ignore the quadruplet.
+ If 6-bonded, require m<k.
+
+ For 4-bonded quadruplets, we can still use k<j, but also
+ assume max(m,j)<i
+ */
+
+ if(three_body_energies || three_body_forces ||
+ four_body_energies || four_body_forces)
+ for(jx = first[i]; jx<first[i+1]; jx++) {
+ fjx = fjy = fjz = 0.0;
+
+ j = nlist_short[jx];
+
+ for(kx = first[i]; kx<jx; kx++) {
+ fkx = fky = fkz = 0.0;
+
+ k = nlist_short[kx];
+
+ /*
+ Search lists of j and k, and see if
+ 1) j is in k-list (closed triplet)
+ 2) j and k have a common neighbor (closed quadruplet)
+ */
+
+ c_ij = c_ki = 1;
+
+ const int sij = (i < j) ? 1 : -1;
+ const int sjk = (j < k) ? 1 : -1;
+ const int ski = (k < i) ? 1 : -1;
+
+
+ T12 = T23 = T31 = 0;
+
+ mj = first[j];
+ /*
+ Since i is in the j-list, and i > k and the list
+ is sorted, the loop below terminates:-)
+ */
+ while(mj < first[j+1] && nlist_short[mj] < k) mj = mj + 1;
+ if(mj < first[j+1] && nlist_short[mj] == k) {
+ /* Closed triplet */
+ c_jk = 1;
+
+ if(j > i) continue; /* Require k<j<i for closed triplets */
+ } else {
+ /* Open triplet */
+ c_jk = 0;
+ }
+
+ tx0 = gettime();
+
+ w3 = get_weight(triclinic,ss[i],ss[j],ss[k]);
+
+ int triplet_defer;
+ if(w3 > 0.0) {
+ triplet_defer = 0;
+
+ dvir_ij = dvir_jk = dvir_ki = 0.0;
+ if(c_ij && c_jk)
+ T12 = get_triplet(xx,j,i,k,&bond_hash,&T12work,&dvir_ij,&dvir_jk);
+ if(c_ki && c_jk)
+ T23 = get_triplet(xx,k,i,j,&bond_hash,&T23work,&dvir_ki,&dvir_jk);
+ if(c_ij && c_ki)
+ T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki);
+
+ if(evflag) {
+ fsave[0][0] = fix; fsave[0][1] = fiy; fsave[0][2] = fiz;
+ fsave[1][0] = fjx; fsave[1][1] = fjy; fsave[1][2] = fjz;
+ fsave[2][0] = fkx; fsave[2][1] = fky; fsave[2][2] = fkz;
+ fix = fiy = fiz = 0.0;
+ fjx = fjy = fjz = 0.0;
+ fkx = fky = fkz = 0.0;
+ }
+
+ tr0 = tr1 = tr2 = tr3 = 0.0;
+ double xvir3t,xvir3v;
+ xvir3t = xvir3v = 0.0;
+
+ if(T12 && T23) {
+ bond_data *bki = bond_hash.Lookup(Doublet(k,i));
+
+ if(three_body_energies && evflag) {
+ tr0 = transtrace(T12->H1H2,bki->H);
+ double dvir = ((dvir_ij + dvir_jk + bki->fl_deriv_sum)*splinepot.vc +
+ splinepot.dvc)*tr0*w3/anorm3;
+ vir3t = vir3t + dvir;
+ xvir3t = xvir3t + dvir;
+ }
+ mcount2++;
+
+ {
+ const double vc = splinepot.vc;
+ tr_trace3(&(bki->H.m[1][0]),
+ &(T12->H1xH2.m[1][0]),&utr1x.d,
+ &(T12->H1yH2.m[1][0]),&utr1y.d,
+ &(T12->H1zH2.m[1][0]),&utr1z.d);
+
+ tr_trace3(&(bki->H.m[1][0]),
+ &(T12->H1H2x.m[1][0]),&utr2x.d,
+ &(T12->H1H2y.m[1][0]),&utr2y.d,
+ &(T12->H1H2z.m[1][0]),&utr2z.d);
+
+ tr_trace3(&(T12->H1H2.m[1][0]),
+ &(bki->Hx.m[1][0]),&utr3x.d,
+ &(bki->Hy.m[1][0]),&utr3y.d,
+ &(bki->Hz.m[1][0]),&utr3z.d);
+
+ if(linalg.single) {
+ trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f;
+ trd1y = utr1y.f; trd2y = utr2y.f; trd3y = utr3y.f;
+ trd1z = utr1z.f; trd2z = utr2z.f; trd3z = utr3z.f;
+ } else {
+ trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d;
+ trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d;
+ trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d;
+ }
+
+ dfix = ( (-sij)*trd1x + ( ski)*trd3x ) * (vc / anorm3);
+ dfjx = ( ( sij)*trd1x + (-sjk)*trd2x ) * (vc / anorm3);
+ dfkx = ( ( sjk)*trd2x + (-ski)*trd3x ) * (vc / anorm3);
+
+ dfiy = ( (-sij)*trd1y + ( ski)*trd3y ) * (vc / anorm3);
+ dfjy = ( ( sij)*trd1y + (-sjk)*trd2y ) * (vc / anorm3);
+ dfky = ( ( sjk)*trd2y + (-ski)*trd3y ) * (vc / anorm3);
+
+ dfiz = ( (-sij)*trd1z + ( ski)*trd3z ) * (vc / anorm3);
+ dfjz = ( ( sij)*trd1z + (-sjk)*trd2z ) * (vc / anorm3);
+ dfkz = ( ( sjk)*trd2z + (-ski)*trd3z ) * (vc / anorm3);
+ }
+
+ if(triplet_debug)
+ force_debug_3t(xx,i,j,k, i,j,k,
+ dfix,dfiy,dfiz,
+ dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz);
+
+ if(three_body_forces)
+ accumulate_forces_3(w3);
+ }
+
+ if(T12 != 0) {
+ //printf("T12 i,j,k = %d,%d,%d\n",i,j,k);
+ mcount++;
+ if(three_body_energies && evflag) {
+ tr1 = transtrace(T12->H1H2,T12->H1H2);
+ double dvir = (2.0*(dvir_ij + dvir_jk)*splinepot.vd +
+ splinepot.dvd)*tr1*w3/anorm4;
+ vir3v = vir3v + dvir;
+ xvir3v = xvir3v + dvir;
+ }
+
+ {
+ const double vd = splinepot.vd;
+
+ tr_trace3(&(T12->H1H2.m[1][0]),
+ &(T12->H1xH2.m[1][0]),&utr1x.d,
+ &(T12->H1yH2.m[1][0]),&utr1y.d,
+ &(T12->H1zH2.m[1][0]),&utr1z.d);
+ tr_trace3(&(T12->H1H2.m[1][0]),
+ &(T12->H1H2x.m[1][0]),&utr2x.d,
+ &(T12->H1H2y.m[1][0]),&utr2y.d,
+ &(T12->H1H2z.m[1][0]),&utr2z.d);
+ if(linalg.single) {
+ trd1x = utr1x.f; trd2x = utr2x.f;
+ trd1y = utr1y.f; trd2y = utr2y.f;
+ trd1z = utr1z.f; trd2z = utr2z.f;
+ } else {
+ trd1x = utr1x.d; trd2x = utr2x.d;
+ trd1y = utr1y.d; trd2y = utr2y.d;
+ trd1z = utr1z.d; trd2z = utr2z.d;
+ }
+
+ dfix = 2.0*(-sij)*trd1x * (vd / anorm4);
+ dfkx = 2.0*( sjk)*trd2x * (vd / anorm4);
+ dfjx = -(dfix + dfkx);
+
+ dfiy = 2.0*(-sij)*trd1y * (vd / anorm4);
+ dfky = 2.0*( sjk)*trd2y * (vd / anorm4);
+ dfjy = -(dfiy + dfky);
+
+ dfiz = 2.0*(-sij)*trd1z * (vd / anorm4);
+ dfkz = 2.0*( sjk)*trd2z * (vd / anorm4);
+ dfjz = -(dfiz + dfkz);
+ }
+
+ if(triplet_debug) /* Compare forces to numerical derivatives */
+ force_debug_3v(xx,i,j,k, j,i,k,
+ dfix,dfiy,dfiz,
+ dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz);
+
+
+ if(three_body_forces)
+ accumulate_forces_3(w3);
+ }
+
+ if(T23 != 0) {
+ //printf("T23 i,j,k = %d,%d,%d\n",i,j,k);
+ mcount++;
+ if(three_body_energies && evflag) {
+ tr2 = transtrace(T23->H1H2,T23->H1H2);
+ double dvir = (2.0*(dvir_jk + dvir_ki)*splinepot.vd +
+ splinepot.dvd)*tr2*w3/anorm4;
+ vir3v = vir3v + dvir;
+ xvir3v = xvir3v + dvir;
+ }
+
+ {
+ const double vd = splinepot.vd;
+
+ tr_trace3(&(T23->H1H2.m[1][0]),
+ &(T23->H1xH2.m[1][0]),&utr1x.d,
+ &(T23->H1yH2.m[1][0]),&utr1y.d,
+ &(T23->H1zH2.m[1][0]),&utr1z.d);
+ tr_trace3(&(T23->H1H2.m[1][0]),
+ &(T23->H1H2x.m[1][0]),&utr2x.d,
+ &(T23->H1H2y.m[1][0]),&utr2y.d,
+ &(T23->H1H2z.m[1][0]),&utr2z.d);
+ if(linalg.single) {
+ trd1x = utr1x.f; trd2x = utr2x.f;
+ trd1y = utr1y.f; trd2y = utr2y.f;
+ trd1z = utr1z.f; trd2z = utr2z.f;
+ } else {
+ trd1x = utr1x.d; trd2x = utr2x.d;
+ trd1y = utr1y.d; trd2y = utr2y.d;
+ trd1z = utr1z.d; trd2z = utr2z.d;
+ }
+
+ dfix = 2.0*( ski)*trd1x * (vd / anorm4);
+ dfjx = 2.0*(-sjk)*trd2x * (vd / anorm4);
+ dfkx = -(dfix + dfjx);
+
+ dfiy = 2.0*( ski)*trd1y * (vd / anorm4);
+ dfjy = 2.0*(-sjk)*trd2y * (vd / anorm4);
+ dfky = -(dfiy + dfjy);
+
+ dfiz = 2.0*( ski)*trd1z * (vd / anorm4);
+ dfjz = 2.0*(-sjk)*trd2z * (vd / anorm4);
+ dfkz = -(dfiz + dfjz);
+ }
+
+ if(triplet_debug) /* Compare forces to numerical derivatives */
+ force_debug_3v(xx,i,j,k, k,i,j,
+ dfix,dfiy,dfiz,
+ dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz);
+
+ if(three_body_forces)
+ accumulate_forces_3(w3);
+
+ }
+
+ if(T31 != 0) {
+ //printf("T31 i,j,k = %d,%d,%d\n",i,j,k);
+ mcount++;
+ if(three_body_energies && evflag) {
+ tr3 = transtrace(T31->H1H2,T31->H1H2);
+ double dvir = (2.0*(dvir_ki + dvir_ij)*splinepot.vd +
+ splinepot.dvd)*tr3*w3/anorm4;
+ vir3v = vir3v + dvir;
+ xvir3v = xvir3v + dvir;
+ }
+
+ {
+ const double vd = splinepot.vd;
+
+ tr_trace3(&(T31->H1H2.m[1][0]),
+ &(T31->H1xH2.m[1][0]),&utr1x.d,
+ &(T31->H1yH2.m[1][0]),&utr1y.d,
+ &(T31->H1zH2.m[1][0]),&utr1z.d);
+ tr_trace3(&(T31->H1H2.m[1][0]),
+ &(T31->H1H2x.m[1][0]),&utr2x.d,
+ &(T31->H1H2y.m[1][0]),&utr2y.d,
+ &(T31->H1H2z.m[1][0]),&utr2z.d);
+ if(linalg.single) {
+ trd1x = utr1x.f; trd2x = utr2x.f;
+ trd1y = utr1y.f; trd2y = utr2y.f;
+ trd1z = utr1z.f; trd2z = utr2z.f;
+ } else {
+ trd1x = utr1x.d; trd2x = utr2x.d;
+ trd1y = utr1y.d; trd2y = utr2y.d;
+ trd1z = utr1z.d; trd2z = utr2z.d;
+ }
+
+ dfjx = 2.0*( sij)*trd1x * (vd / anorm4);
+ dfkx = 2.0*(-ski)*trd2x * (vd / anorm4);
+ dfix = -(dfjx + dfkx);
+
+ dfjy = 2.0*( sij)*trd1y * (vd / anorm4);
+ dfky = 2.0*(-ski)*trd2y * (vd / anorm4);
+ dfiy = -(dfjy + dfky);
+
+ dfjz = 2.0*( sij)*trd1z * (vd / anorm4);
+ dfkz = 2.0*(-ski)*trd2z * (vd / anorm4);
+ dfiz = -(dfjz + dfkz);
+
+ }
+
+ if(triplet_debug) /* Compare forces to numerical derivatives */
+ force_debug_3v(xx,i,j,k, i,j,k,
+ dfix,dfiy,dfiz,
+ dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz);
+
+ if(three_body_forces)
+ accumulate_forces_3(w3);
+ }
+
+ v33 = tr0 / anorm3;
+ v43 = (tr1 + tr2 + tr3) / anorm4;
+ double de_triplet = (splinepot.vc*v33 + splinepot.vd*v43) * e_scale * w3;
+ e_triplet = e_triplet + de_triplet;
+ e_triplet_c = e_triplet_c + splinepot.vc*v33 * e_scale * w3;
+ c_t++;
+
+ //printf("xxxx %6d %6d %6d :: %20.10e\n",1,2,3,de_triplet);
+
+ if(evflag) {
+ double drji[3],drki[3];
+ double fj[3] = {fjx,fjy,fjz},fk[3] = {fkx,fky,fkz};
+ for(int p = 0; p<3; p++) {
+ drji[p] = xx[j][p] - xx[i][p];
+ drki[p] = xx[k][p] - xx[i][p];
+ /* To fix stress-per-atom scaling. */
+ fj[p] *= e_scale;
+ fk[p] *= e_scale;
+ }
+
+ ev_tally3(i,j,k,de_triplet,0.0,fj,fk,drji,drki);
+
+ if(volpres_flag && vflag_atom) {
+ //virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale;
+ double dvir = -(xvir3v + xvir3t) * rhoinv*e_scale * (1.0/3.0);
+ for(int pp = 0; pp<3; pp++) {
+ vatom[i][pp] += dvir;
+ vatom[j][pp] += dvir;
+ vatom[k][pp] += dvir;
+ }
+ }
+
+ fix = fix+fsave[0][0]; fiy = fiy+fsave[0][1]; fiz = fiz+fsave[0][2];
+ fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2];
+ fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2];
+ }
+
+ tx1 = gettime();
+ ttriplet += tx1 - tx0;
+ nttriplet++;
+ } else {
+ triplet_defer = 1;
+ }
+
+ if(four_body_energies || four_body_forces)
+ if(j < i) { /* Search for quadruplet */
+ tx0 = gettime();
+
+ mj = first[j];
+ mk = first[k];
+ /*
+ i is in both the j-list and the k-list, and i > k,
+ and lists are sorted, so the loop terminates.
+ */
+ while(nlist_short[mj] < i && nlist_short[mk] < i) {
+
+ if(mj >= first[j+1] || mk >= first[k+1]) {
+ printf("Illegal quad...\n"
+ " j=%d first[j]=%d first[j+1]=%d mj=%d\n"
+ " k=%d first[k]=%d first[k+1]=%d mk=%d\n",
+ j,first[j],first[j+1],mj,
+ k,first[k],first[k+1],mk);
+ error->one(__FILE__,__LINE__,"Shit, brkoen quad loop");
+ }
+
+ if(nlist_short[mj] == nlist_short[mk]) {
+ /* Closed quadruplet */
+ m = nlist_short[mj];
+ c_jm = c_km = 1;
+
+ const int sim = (i < m) ? 1 : -1;
+ const int sjm = (j < m) ? 1 : -1;
+ const int skm = (k < m) ? 1 : -1;
+
+ w4 = get_weight(triclinic,ss[i],ss[j],ss[k],ss[m]);
+
+ if(w4 > 0.0) {
+
+ /* Alrady know ij,jk,ki,jm,km bonds. Look for im bond. */
+ mi = first[i];
+ while(mi < first[i+1] && nlist_short[mi] < m) mi = mi + 1;
+ if(mi < first[i+1] && nlist_short[mi] == m)
+ c_im = 1;
+ else
+ c_im = 0;
+
+ if(c_im == 0 || c_jk == 0 || (c_jk && c_im && m < k)) {
+
+ if(triplet_defer) {
+ dvir_ij = dvir_jk = dvir_ki = 0.0;
+ if(c_ij && c_jk)
+ T12 = get_triplet(xx,j,i,k,&bond_hash,&T12work,&dvir_ij,&dvir_jk);
+ if(c_ki && c_jk)
+ T23 = get_triplet(xx,k,i,j,&bond_hash,&T23work,&dvir_ki,&dvir_jk);
+ if(c_ij && c_ki)
+ T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki);
+ triplet_defer = 0;
+ }
+
+
+ fmx = fmy = fmz = 0.0;
+ double xvir4 = 0.0;
+
+ if(evflag) {
+ fsave[0][0] = fix; fsave[0][1] = fiy; fsave[0][2] = fiz;
+ fsave[1][0] = fjx; fsave[1][1] = fjy; fsave[1][2] = fjz;
+ fsave[2][0] = fkx; fsave[2][1] = fky; fsave[2][2] = fkz;
+ fsave[3][0] = fmx; fsave[3][1] = fmy; fsave[3][2] = fmz;
+ fix = fiy = fiz = 0.0;
+ fjx = fjy = fjz = 0.0;
+ fkx = fky = fkz = 0.0;
+ fmx = fmy = fmz = 0.0;
+ }
+
+ tr1 = tr2 = tr3 = 0.0;
+
+ dvir_im = dvir_jm = dvir_km = 0.0;
+ T45 = T56 = T64 = 0;
+ if(T12 != 0 && c_km && c_im)
+ T45 = get_triplet(xx,m,i,k,&bond_hash,&T45work,&dvir_im,&dvir_km);
+ if(T23 != 0 && c_im && c_jm)
+ T56 = get_triplet(xx,m,i,j,&bond_hash,&T56work,&dvir_im,&dvir_jm);
+ if(T31 != 0 && c_jm && c_km)
+ T64 = get_triplet(xx,m,j,k,&bond_hash,&T64work,&dvir_jm,&dvir_km);
+
+ if(T12 != 0 && T45 != 0) {
+ if(four_body_energies && evflag) {
+ tr1 = transtrace(T12->H1H2,T45->H1H2);
+ double dvir = ( (dvir_ij + dvir_jk + dvir_im + dvir_km)*splinepot.ve +
+ splinepot.dve )*tr1*w4/anorm4;
+ vir4 = vir4 + dvir;
+ xvir4 = xvir4 + dvir;
+ }
+ qcount++;
+
+ {
+ const double ve = splinepot.ve;
+
+ trd_update_4(T12,T45);
+
+ dfix_update_4a(x);
+ dfix_update_4a(y);
+ dfix_update_4a(z);
+ }
+
+ if(quad_debug) /* Compare forces to numerical derivatives */
+ force_debug_4(xx,i,j,k,m, i,j,k,m,
+ dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
+
+ if(four_body_forces)
+ accumulate_forces_4(w4);
+ }
+
+ if(T23 != 0 && T56 != 0) {
+ if(four_body_energies && evflag) {
+ tr2 = transtrace(T23->H1H2,T56->H1H2);
+ double dvir = ( (dvir_ki + dvir_jk + dvir_im + dvir_jm)*splinepot.ve +
+ splinepot.dve )*tr2*w4/anorm4;
+ vir4 = vir4 + dvir;
+ xvir4 = xvir4 + dvir;
+ }
+ qcount++;
+
+ {
+ const double ve = splinepot.ve;
+
+ trd_update_4(T23,T56);
+
+ dfix_update_4b(x);
+ dfix_update_4b(y);
+ dfix_update_4b(z);
+ }
+
+ if(quad_debug) /* Compare forces to numerical derivatives */
+ force_debug_4(xx,i,j,k,m, i,m,j,k,
+ dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
+
+ if(four_body_forces)
+ accumulate_forces_4(w4);
+
+ }
+
+ if(T31 != 0 && T64 != 0) {
+ if(four_body_energies && evflag) {
+ tr3 = transtrace(T31->H1H2,T64->H1H2);
+ double dvir = ( (dvir_ki + dvir_ij + dvir_jm + dvir_km)*splinepot.ve +
+ splinepot.dve )*tr3*w4/anorm4;
+ vir4 = vir4 + dvir;
+ xvir4 = xvir4 + dvir;
+ }
+ qcount++;
+
+ {
+ const double ve = splinepot.ve;
+
+ /* X */
+ trd_update_4(T31,T64);
+
+ dfix_update_4c(x);
+ dfix_update_4c(y);
+ dfix_update_4c(z);
+ }
+
+ if(quad_debug) /* Compare forces to numerical derivatives */
+ force_debug_4(xx,i,j,k,m, i,j,m,k,
+ dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
+ dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
+
+ if(four_body_forces)
+ accumulate_forces_4(w4);
+ }
+
+ double de_quad = splinepot.ve*(tr1 + tr2 + tr3)/anorm4 * e_scale * w4;
+ e_quad = e_quad + de_quad;
+ if((T12 && T45) ||
+ (T23 && T56) ||
+ (T31 && T64)) {
+ c_q++;
+ }
+
+ if(evflag) {
+ double drim[3],drjm[3],drkm[3];
+ double fi[3] = {fix,fiy,fiz};
+ double fj[3] = {fjx,fjy,fjz};
+ double fk[3] = {fkx,fky,fkz};
+ for(int p = 0; p<3; p++) {
+ drim[p] = xx[i][p] - xx[m][p];
+ drjm[p] = xx[j][p] - xx[m][p];
+ drkm[p] = xx[k][p] - xx[m][p];
+ fi[p] *= e_scale;
+ fj[p] *= e_scale;
+ fk[p] *= e_scale;
+ }
+
+ ev_tally4(i,j,k,m,de_quad,fi,fj,fk,drim,drjm,drkm);
+
+ if(volpres_flag && vflag_atom) {
+ //virial[i] = virial[i] - vir4 * rhoinv*e_scale;
+ double dvir = -xvir4 * rhoinv*e_scale * (1.0/4.0);
+ for(int pp = 0; pp<3; pp++) {
+ vatom[i][pp] += dvir;
+ vatom[j][pp] += dvir;
+ vatom[k][pp] += dvir;
+ vatom[m][pp] += dvir;
+ }
+ }
+
+ fix = fix+fsave[0][0]; fiy = fiy+fsave[0][1]; fiz = fiz+fsave[0][2];
+ fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2];
+ fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2];
+ fmx = fmx+fsave[3][0]; fmy = fmy+fsave[3][1]; fmz = fmz+fsave[3][2];
+ }
+
+ ff[m][0] += fmx * e_scale;
+ ff[m][1] += fmy * e_scale;
+ ff[m][2] += fmz * e_scale;
+
+ }
+ }
+ mj = mj + 1;
+ mk = mk + 1;
+ } else if(nlist_short[mj] < nlist_short[mk]) {
+ mj = mj + 1;
+ } else {
+ mk = mk + 1;
+ }
+
+ }
+ tx1 = gettime();
+ tquad += tx1 - tx0;
+ ntquad++;
+ ntquaditer++;
+ }
+
+
+ ff[k][0] += fkx * e_scale;
+ ff[k][1] += fky * e_scale;
+ ff[k][2] += fkz * e_scale;
+
+ }
+#undef transtrace
+
+ ff[j][0] += fjx * e_scale;
+ ff[j][1] += fjy * e_scale;
+ ff[j][2] += fjz * e_scale;
+
+ }
+
+ ff[i][0] += fix * e_scale;
+ ff[i][1] += fiy * e_scale;
+ ff[i][2] += fiz * e_scale;
+
+ if(single_energies == 1 && i < nloc) {
+ const double evol0 = splinepot.evol0;
+ if(eflag_global) {
+ e_single = e_single + evol0 * e_scale;
+ eng_vdwl = eng_vdwl + evol0 * e_scale;
+ }
+ if(eflag_atom) eatom[i] = eatom[i] + evol0 * e_scale;
+ if(volpres_flag && vflag_atom) {
+ for(int pp = 0; pp<3; pp++)
+ vatom[i][pp] = vatom[i][pp] - rhoinv*splinepot.devol0*e_scale;
+ }
+
+ }
+
+ }
+
+ tx0 = gettime();
+ for(i = 0; i<ntot; i++)
+ for(p = 0; p<3; p++)
+ atom->f[i][p] = atom->f[i][p] + ff[i][p];
+
+ memory->sfree(nlist_short);
+ memory->sfree(first);
+ if(ss != xx) memory->sfree(ss);
+ memory->sfree(ff);
+ memory->sfree(xx);
+ tx1 = gettime();
+ tmem += tx1-tx0;
+ ntmem++;
+
+ t1 = gettime(1);
+
+ //printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q);
+
+
+#ifdef TIMING_ON
+ if(comm->me == 0) {
+ double tsum = (tmem+tsort+tpair+tlookup+ttriplet+tquad);
+ double nsum = (ntmem+ntsort+ntpair+ntlookup+nttriplet+ntquad);
+ //double adj = ((t1-t0)-tsum)/nsum;
+ /* Use adj = 6ns for RDTSC, and 58ns for gettimeofday,
+ on monkfish.llnl.gov, 2.4GHz Intel
+
+ Use adj = 35.945ns for RDTSC on uBGL (assumed rate set to 700MHz)
+ */
+ double adj = 35.945e-9;
+
+ double
+ memadj = tmem - adj*ntmem ,
+ sortadj = tsort - adj*ntsort ,
+ pairadj = tpair - adj*ntpair ,
+ lookupadj = tlookup - adj*ntlookup ,
+ tripletadj = ttriplet - adj*nttriplet,
+ quadadj = tquad - adj*ntquad ,
+
+ make_b_adj = t_make_b - adj*n_make,
+ make_t_adj = t_make_t - adj*n_make,
+ make_b2_adj = t_make_b2 - adj*n_make_b2,
+ trace_adj = t_trace - adj*n_trace;
+
+ printf("mgpt engy = %10.3fms\n",(t1-t0)*1e3);
+ printf(" mem = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ tmem*1e3,ntmem,memadj*1e3,memadj/ntmem*1e9);
+ printf(" sort = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ tsort*1e3,ntsort,sortadj*1e3,sortadj/ntsort*1e9);
+ printf(" pair = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ tpair*1e3,ntpair,pairadj*1e3,pairadj/ntpair*1e9);
+ printf(" lookup = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ tlookup*1e3,ntlookup,lookupadj*1e3,lookupadj/ntlookup*1e9);
+ printf(" triplet = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ ttriplet*1e3,nttriplet,tripletadj*1e3,tripletadj/nttriplet*1e9);
+ printf(" quad = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ tquad*1e3,ntquaditer,quadadj*1e3,quadadj/ntquaditer*1e9);
+ printf(" sum = %10.3fms adj = %10.3fms\n",
+ tsum*1e3,(tsum - adj*nsum)*1e3);
+ printf("\n make_b = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ t_make_b*1e3,n_make,make_b_adj*1e3,make_b_adj/n_make*1e9);
+ printf(" make_b2 = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
+ t_make_b2*1e3,n_make_b2,make_b2_adj*1e3,make_b2_adj/n_make_b2*1e9);
+ printf(" make_t = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n\n",
+ t_make_t*1e3,n_make,make_t_adj*1e3,make_t_adj/n_make*1e9);
+ printf(" trace = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n\n",
+ t_trace*1e3,n_trace,trace_adj*1e3,trace_adj/n_trace*1e9);
+
+ printf("mcount (transpose + trace for triplet) = %.0f , %.0f qcount = %.0f lmax = %d\n",
+ mcount,mcount2,qcount,lmax);
+
+ printf("nbc=%.0f tbl=%.3fms tbm=%.3fms one tbl=%.3fns one tbm=%.3fns\n",
+ nbc,(tbl-adj*nbc)*1e3,(tbm-adj*nbc)*1e3,(tbl/nbc-adj)*1e9,
+ (tbm/nbc-adj)*1e9);
+ printf("\n\nForces:\n");
+ printf("fix = %.3f fiy=%.3f fiz=%.3f\n",fix,fiy,fiz);
+ printf("fjx = %.3f fjy=%.3f fjz=%.3f\n",fjx,fjy,fjz);
+ printf("fkx = %.3f fky=%.3f fkz=%.3f\n",fkx,fky,fkz);
+ printf("\n");
+
+ printf("Bonds : nsearch=%d maxlen=%d avg.len=%.3f\n",
+ bond_hash.NSearch(),bond_hash.MaxLength(),
+ bond_hash.NStep()/(double) bond_hash.NSearch());
+
+ printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q);
+
+ printf("@@ Total number of trace3 calls is %d, total number of make_triplet is %.1f\n",
+ ntr_calls,n_make);
+
+ {
+ Hash<bond_data,Doublet>::Iterator iter = bond_hash.begin();
+ int nitem = 0,nhit = 0;
+ while(iter != bond_hash.end()) {
+ nitem++;
+ nhit += iter.link()->hits;
+ iter.next();
+ }
+ printf("bond_hash hits: nitems=%d nhits=%d hits/item = %.3f\n",
+ nitem,nhit,nhit/(double) nitem);
+ }
+ }
+#endif
+
+ if(volpres_flag) {
+ /*
+ Include contributions to the pressure due to derivatines
+ of the energy with respect to the potential input volume.
+ */
+
+ /* The following lines have moved to beginning of functions,
+ since they are used in calculating per-atom virial contributions */
+ /*
+ double vtot = 1.0;
+ double ntot = atom->natoms;
+ for(i = 0; i<3; i++)
+ vtot = vtot * (domain->boxhi[i] - domain->boxlo[i]);
+ double rhoinv = vtot / ntot;
+ */
+
+ if(single_energies) // Virial correction for self energy
+ for(i = 0; i<3; i++) {
+ //virial[i] = virial[i] + nloc*pot_input_vol*pvol0*e_scale;
+ virial[i] = virial[i] - nloc*rhoinv*splinepot.devol0*e_scale;
+ }
+
+ if(pair_energies) // Virial correction for pair energy
+ for(i = 0; i<3; i++)
+ virial[i] = virial[i] + rhoinv*e_scale*volvir2;
+
+ if(three_body_energies) // Virial correction for three body enegries
+ for(i = 0; i<3; i++) {
+ //virial[i] = virial[i] - pot_input_vol*(e_triplet_c*pc + (e_triplet-e_triplet_c)*pd);
+ virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale;
+ }
+
+ if(four_body_energies) // Virial correction for four body enegries
+ for(i = 0; i<3; i++) {
+ //virial[i] = virial[i] - pot_input_vol*e_quad*pe;
+ virial[i] = virial[i] - vir4 * rhoinv*e_scale;
+ }
+
+ }
+
+ *e_s = e_single;
+ *e_p = e_pair;
+ *e_t = e_triplet;
+ *e_q = e_quad;
+}
+
+void PairMGPT::compute(int eflag, int vflag)
+{
+ if(eflag || vflag) ev_setup(eflag, vflag);
+ else evflag = vflag_fdotr = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
+
+ int newton_pair = force->newton_pair;
+ double e_s,e_p,e_t,e_q;
+
+ //printf("newton_pair = %d, newton = %d, tag_enable = %d\n",force->newton_pair,force->newton,atom->tag_enable);
+
+ if(newton_pair == 0) {
+ printf("This is a problem. MGPT requires newton_pair flag to be on. Exiting...\n");
+ exit(1);
+ }
+
+ if(atom->tag_enable == 0) {
+ printf("This is a problem. MGPT requires tag_enable flag to be on. Exiting...\n");
+ exit(1);
+ }
+
+ compute_x(listfull->numneigh,listfull->firstneigh,&e_s,&e_p,&e_t,&e_q,evflag,newton_pair);
+
+ if(0) { // Stupid force calculation / verification
+ int ii,nmax=-1;
+ for(ii = 0; ii<listfull->inum + listfull->gnum; ii++) {
+ int i = listfull->ilist[ii];
+ if(i > nmax) nmax = i;
+ }
+ nmax++;
+ double *ffwork = new double[3*nmax];
+ double *ffloc = new double[3*listfull->inum];
+ double *ffloc2 = new double[3*listfull->inum];
+ double **ffptr = new double *[nmax];
+ for(ii = 0; ii<listfull->inum + listfull->gnum; ii++)
+ ffptr[ii] = &ffwork[3*ii];
+
+ printf("Computing boundary forces\n");
+ for(ii = 0; ii<listfull->inum; ii++) {
+ ffloc2[3*ii] = 0.0;
+ ffloc2[3*ii+1] = 0.0;
+ ffloc2[3*ii+2] = 0.0;
+ int i = listfull->ilist[ii];
+ for(int jj = 0; jj<listfull->inum+listfull->gnum; jj++) {
+ int j = listfull->ilist[jj];
+ if(atom->tag[i] == atom->tag[j])
+ for(int p = 0; p<3; p++)
+ ffloc2[3*ii+p] += atom->f[j][p];
+ }
+ }
+
+ printf("Starting main displacement force calculation\n");
+ for(ii = 0; ii<listfull->inum; ii++) {
+ int i = listfull->ilist[ii];
+
+ double **atom_f_save = atom->f;
+ atom->f = ffptr;
+
+ for(int p = 0; p<3; p++) {
+ double xsave = atom->x[i][p];
+ const double delta = 1e-3;
+
+ atom->x[i][p] = xsave + delta;
+ for(int jj = 0; jj<3*nmax; jj++) ffwork[jj] = 0.0;
+ compute_x(listfull->numneigh,
+ listfull->firstneigh,
+ &e_s,&e_p,&e_t,&e_q,evflag,newton_pair);
+ double e1 = e_s + e_p + e_t + e_q;
+
+ atom->x[i][p] = xsave - delta;
+ for(int jj = 0; jj<3*nmax; jj++) ffwork[jj] = 0.0;
+ compute_x(listfull->numneigh,
+ listfull->firstneigh,
+ &e_s,&e_p,&e_t,&e_q,evflag,newton_pair);
+ double e2 = e_s + e_p + e_t + e_q;
+
+ ffloc[3*ii+p] = -(e1-e2)/(2*delta);
+
+ atom->x[i][p] = xsave;
+ }
+
+ atom->f = atom_f_save;
+ printf("Force on i=%4d:\n",i);
+ printf(" Position %20.10e %20.10e %20.10e\n",
+ atom->x[i][0],atom->x[i][1],atom->x[i][2]);
+ printf(" Exact %20.10e %20.10e %20.10e\n",
+ atom->f[i][0],atom->f[i][1],atom->f[i][2]);
+ printf(" Numerical %20.10e %20.10e %20.10e\n",
+ ffloc[3*ii+0],ffloc[3*ii+1],ffloc[3*ii+2]);
+ printf(" Boundary %20.10e %20.10e %20.10e\n",
+ ffloc2[3*ii+0],ffloc2[3*ii+1],ffloc2[3*ii+2]);
+ }
+
+
+ delete[] ffloc2;
+ delete[] ffloc;
+ delete[] ffptr;
+ delete[] ffwork;
+ }
+
+
+ if(0) {
+ printf("\nForces MGPT:\n");
+ const int iimax = (listfull->inum < 10) ? listfull->inum : 10;
+ for(int ii = 0; ii<iimax; ii++) {
+ int i = listfull->ilist[ii];
+ printf("%4d = %20.10e %20.10e %20.10e\n",
+ i,atom->f[i][0],atom->f[i][1],atom->f[i][2]);
+ }
+ printf("\n\n");
+ }
+
+ if(vflag_fdotr) {
+ //printf("##### Using virial_compute!!!\n");
+ virial_fdotr_compute();
+ }
+}
+
+void PairMGPT::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for(int i = 0; i <= n; i++)
+ for(int j = 0; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ memory->create(cutghost,n+1,n+1,"pair:cutsq");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+void PairMGPT::settings(int narg, char **arg)
+{
+ if(narg != 0) error->all(__FILE__,__LINE__,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairMGPT::coeff(int narg, char **arg)
+{
+ int single_precision = 0;
+
+ if(narg < 5)
+ error->all(__FILE__,__LINE__,
+ "Not enough arguments for mgpt (MGPT) pair coefficients.");
+
+ if(!allocated) allocate();
+
+ // Make sure I,J args are * *
+ if(strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+ error->all(__FILE__,__LINE__,"Incorrect args for pair coefficients");
+
+ double vol;
+ if(sscanf(arg[4], "%lg", &vol) != 1 || vol <= 0.0)
+ error->all(__FILE__,__LINE__,"Invalid volume in mgpt (MGPT) pair coefficients.");
+
+ volpres_flag = 1;
+ single_precision = 0;
+
+ /* Parse arguments */ {
+ int volpres_tag = 0,precision_tag = 0,nbody_tag = 0;
+
+ int iarg = 5;
+ while (iarg < narg) {
+ if(strcmp(arg[iarg],"volpress") == 0) { /* Volumetric pressure flag */
+ if (iarg+2 > narg)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if(strcmp(arg[iarg+1],"yes") == 0) volpres_flag = 1;
+ else if(strcmp(arg[iarg+1],"no") == 0) volpres_flag = 0;
+ else {
+ char line[1024];
+ sprintf(line,"(In %s:%d) Invalid value for volumetric pressure argument.\n"
+ "It should be \"volpress yes\" or \"volpress no\".\n"
+ "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]);
+ error->all(__FILE__,__LINE__,line);
+ }
+ volpres_tag = 1;
+ iarg += 2;
+ if(comm->me == 0) printf("* volpress: volpres_flag = %d [%s %s]\n",volpres_flag,arg[iarg-2],arg[iarg-1]);
+ } else if(strcmp(arg[iarg],"nbody") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if(strspn(arg[iarg+1],"1234") == strlen(arg[iarg+1])) {
+ nbody_flag = 0;
+ for(int i = 0; i<4; i++)
+ if(strchr(arg[iarg+1],'1'+i) != NULL) {
+ nbody_flag = nbody_flag + (1<<i);
+ if(comm->me == 0) printf("Explicitly adding %d-tuple forces.\n",i+1);
+ }
+ } else {
+ char line[1024];
+ sprintf(line,"(In %s:%d) Invalid value for nbody flag.\n"
+ "It should be e.g. \"nbody=1234\" (for single, pair, triple, and quad forces/energiers)\n"
+ "For e.g. only pair and triple forces/energies, use \"nbody=23\".\n"
+ "The default is \"nbody=1234\".\n"
+ "The current value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]);
+ error->all(__FILE__,__LINE__,line);
+ }
+ nbody_tag = 1;
+ iarg += 2;
+ } else if(strcmp(arg[iarg],"precision") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if(strcmp(arg[iarg+1],"single") == 0) single_precision = 1;
+ else if(strcmp(arg[iarg+1],"double") == 0) single_precision = 0;
+ else {
+ char line[1024];
+ sprintf(line,"(In %s:%d) Invalid value for precision argument.\n"
+ "It should be \"precision single\" or \"precision double\".\n"
+ "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]);
+ error->all(__FILE__,__LINE__,line);
+ }
+ precision_tag = 1;
+ iarg += 2;
+ if(comm->me == 0) printf("* precision: single_flag = %d [%s %s]\n",single_precision,arg[iarg-2],arg[iarg-1]);
+ } else {
+ char line[1024];
+ sprintf(line,"(In %s:%d) Invalid argument. Allowed arguments are:\n"
+ " volpress {yes|no} , default = yes\n"
+ " precision {single|double} , default = double\n"
+ " nbody {[1234,]*} , default = whichever terms potential require\n"
+ "The invalid argument is \"%s\".\n",__FILE__,__LINE__,arg[iarg]);
+ error->all(__FILE__,__LINE__,line);
+ }
+ }
+
+ if(comm->me == 0)
+ printf("Volumetric pressure is %s.\n",volpres_flag ? "on" : "off");
+
+ if(comm->me == 0) {
+ FILE *parmin_fp = force->open_potential(arg[2]);
+ FILE *potin_fp = force->open_potential(arg[3]);
+ if (parmin_fp == NULL || potin_fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open MGPT potential files %s %s",arg[2],arg[3]);
+ error->one(FLERR,str);
+ }
+ fclose(parmin_fp);
+ fclose(potin_fp);
+
+ splinepot.readpot(arg[2],arg[3],vol);
+ printf("evol0 = %.10e\n",splinepot.evol0);
+
+ /* Set up default and requested nbody forces to include */ {
+ int nbody_default = (1<<0) + (1<<1) + (1<<2) + (1<<3);
+
+ if(splinepot.vd == 0.0 && splinepot.dvd == 0.0)
+ nbody_default -= (1<<2); // No 3-body contributions
+ if(splinepot.ve == 0.0 && splinepot.dve == 0.0)
+ nbody_default -= (1<<3); // No 4-body contributions
+
+ if(nbody_tag == 0) nbody_flag = nbody_default;
+
+ if(nbody_flag != nbody_default) {
+ printf("Warning: nbody=%d (suggested=%d) set to disregard multibody-forces in potential.\n",
+ nbody_flag,nbody_default);
+ }
+ }
+ }
+ }
+
+ MPI_Bcast(&nbody_flag,sizeof(nbody_flag),MPI_BYTE,0,world);
+
+ /*
+ Broadcast structure to all processes. In receiving
+ processes, pointes will be screwed up. We allocate
+ memory, and then broadcast contents of arrays.
+ */
+ MPI_Bcast(&splinepot,sizeof(splinepot),MPI_BYTE,0,world);
+ if(comm->me != 0) {
+ splinepot.vpair_spline = new double[splinepot.nr-1][4];
+ splinepot.dvpair_spline = new double[splinepot.nr-1][4];
+ }
+ MPI_Bcast(splinepot.vpair_spline,4*(splinepot.nr-1),MPI_DOUBLE,0,world);
+ MPI_Bcast(splinepot.dvpair_spline,4*(splinepot.nr-1),MPI_DOUBLE,0,world);
+ anorm3 = splinepot.anorm3;
+ anorm4 = splinepot.anorm4;
+ lmax = splinepot.lmax;
+ lang = splinepot.lang;
+ //ipot = splinepot.ipot;
+ for(int i = 0; i<(int) (sizeof(ddl)/sizeof(double)); i++)
+ ddl[i] = splinepot.ddl[i];
+ for(int i = 0; i<lmax; i++) {
+ for(int j = 0; j<lmax; j++)
+ del0.m[i+1][j+1] = 0.0;
+ del0.m[i+1][i+1] = 1.0;
+ }
+
+ /* Set matrix param, cutoff, LAMMPS param */
+ Matrix::sz = lmax;
+
+ rcrit = splinepot.rcrit;
+ rmax = splinepot.rmax;
+ cutoff = rmax;
+ if(rcrit > rmax) cutoff = rcrit;
+
+ // Set LAMMPS pair interaction flags.
+ for(int i = 1; i <= atom->ntypes; i++) {
+ for(int j = 1; j <= atom->ntypes; j++) {
+ setflag[i][j] = 1;
+ cutsq[i][j] = cutoff;
+ cutghost[i][j] = cutoff;
+ }
+ }
+
+ // Set atomic mass.
+ for(int i = 1; i <= atom->ntypes; i++)
+ atom->set_mass(i, splinepot.mass);
+
+ // Initialize linear algebra routines.
+ linalg = mgpt_linalg(lmax,single_precision);
+ if(comm->me == 0)
+ printf("%s",linalg.msg);
+}
+
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+void PairMGPT::init_style()
+{
+ if(force->newton_pair == 0)
+ error->all(__FILE__,__LINE__,"Pair style mgpt requires newton pair on.");
+
+ // Need full neighbor list.
+ int irequest_full = neighbor->request(this);
+ neighbor->requests[irequest_full]->id = 1;
+ neighbor->requests[irequest_full]->half = 0;
+ neighbor->requests[irequest_full]->full = 1;
+ neighbor->requests[irequest_full]->ghost = 1;
+
+ // Also need half neighbor list.
+ int irequest_half = neighbor->request(this);
+ neighbor->requests[irequest_half]->id = 2;
+ neighbor->requests[irequest_half]->half = 0;
+ neighbor->requests[irequest_half]->half_from_full = 1;
+ neighbor->requests[irequest_half]->otherlist = irequest_full;
+
+}
+
+/* ----------------------------------------------------------------------
+ neighbor callback to inform pair style of neighbor list to use
+ half or full
+------------------------------------------------------------------------- */
+void PairMGPT::init_list(int id, NeighList *ptr)
+{
+ if(id == 1) listfull = ptr;
+ else if(id == 2) listhalf = ptr;
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+double PairMGPT::init_one(int i, int j)
+{
+ return cutoff;
+}
+
+/************************************************************************
+ **** REIMPLEMENTATION OF FL AND HAMLTN WITH ANALYTICAL DERIVATIVES ****
+ ************************************************************************/
+/*
+ Reimplementation of bond length potential, including
+ derivatives with respect to x,y, and z.
+*/
+void PairMGPT::fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
+ double &fl_0,double &fl_x,double &fl_y,double &fl_z,
+ double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al) {
+ const double rp = splinepot.rp,p1 = splinepot.p1,r0 = splinepot.r00,al = splinepot.al;
+ const int mode = splinepot.mode;
+ const double pn = splinepot.pn;
+
+ double t,tx,ty,tz,t_rp_ti,t_p1_ti;
+ double s;
+
+ /*
+ // Original code
+ double term;
+ double pn=1.0;
+ if (mode <= 4)
+ term = pow(rp/r, p1);
+ else
+ term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn);
+ */
+
+ double rpi = 1.0/rp;
+ if(mode <= 4) {
+ t = pow(rp*ri,p1);
+ s = -p1 * t * ri;
+ t_rp_ti = p1*rpi;
+ t_p1_ti = log(rp*ri);
+ } else {
+ if(pn == 1.0) {
+ double p1_rpi = -p1*rpi;
+ t = exp(p1 + r*p1_rpi);
+ s = p1_rpi * t;
+ t_rp_ti = -r*p1_rpi*rpi;
+ t_p1_ti = 1.0 - r*rpi;
+ } else {
+ double pni = 1.0/pn;
+ double rprpn = pow(r*rpi,pn);
+ t = exp(-p1*pni*(rprpn - 1.0));
+ s = -p1*rprpn*ri * t;
+ t_rp_ti = p1*rprpn*rpi;
+ t_p1_ti = pni - pni*rprpn;// -pni*(rprpn - 1.0);
+ }
+ }
+ tx = s * xhat;
+ ty = s * yhat;
+ tz = s * zhat;
+
+ fl_rp = t_rp_ti;
+ fl_p1 = t_p1_ti;
+
+ if (r <= r0) {
+ fl_0 = t;
+ fl_x = tx;
+ fl_y = ty;
+ fl_z = tz;
+
+ fl_r0 = 0.0;
+ fl_al = 0.0;
+ } else {
+ double q,qx,qy,qz,exp_q,q_r0,q_al;
+ double r0i,u;
+
+ r0i = 1.0/r0;
+ u = r*r0i - 1.0;
+ q = al*u*u;
+ s = 2*al*u*r0i;
+ qx = s * xhat;
+ qy = s * yhat;
+ qz = s * zhat;
+ q_r0 = -2.0*al*u*r*r0i*r0i;
+ q_al = u*u;
+
+ exp_q = exp(-q);
+ if(mode <= 2) {
+ fl_0 = exp_q * t;
+ fl_x = exp_q*(tx - t*qx);
+ fl_y = exp_q*(ty - t*qy);
+ fl_z = exp_q*(tz - t*qz);
+
+ fl_r0 = -q_r0;
+ fl_al = -q_al;
+ } else {
+ fl_0 = exp_q * (1.0 + q) * t;
+ fl_x = exp_q * (tx + q*(tx - t*qx));
+ fl_y = exp_q * (ty + q*(ty - t*qy));
+ fl_z = exp_q * (tz + q*(tz - t*qz));
+
+ fl_r0 = -q_r0 * q/(1.0 + q);
+ fl_al = -q_al * q/(1.0 + q);
+ }
+ }
+}
+
+
+/*
+ Macros to build elements of the bond matrix, and also
+ its derivatives with repsect to x,y, and z.
+*/
+#define MAKE_ELEMENT_5(i,j) \
+ do { \
+ const double dl0 = del0.m[i][j]; \
+ const double dl4 = gsl_##i * gsl_##j; \
+ const double dl4x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \
+ const double dl4y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \
+ const double dl4z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \
+ \
+ const double tmp = w4*dl4 + w2*dl2 + w0*dl0; \
+ const double tmpx = w4*dl4x + w2*dl2x; \
+ const double tmpy = w4*dl4y + w2*dl2y; \
+ const double tmpz = w4*dl4z + w2*dl2z; \
+ const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \
+ M [j][i] = M[i][j] = fl *tmp; \
+ Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \
+ My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \
+ Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \
+ } while(0)
+
+#define MAKE_ELEMENT_7(i,j) \
+ do { \
+ const double dl0 = del0.m[i][j]; \
+ const double dl6 = gsl_##i * gsl_##j; \
+ const double dl6x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \
+ const double dl6y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \
+ const double dl6z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \
+ \
+ const double tmp = w6*dl6 + w4*dl4 + w2*dl2 + w0*dl0; \
+ const double tmpx = w6*dl6x + w4*dl4x + w2*dl2x; \
+ const double tmpy = w6*dl6y + w4*dl4y + w2*dl2y; \
+ const double tmpz = w6*dl6z + w4*dl4z + w2*dl2z; \
+ const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \
+ M [j][i] = M[i][j] = fl *tmp; \
+ Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \
+ My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \
+ Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \
+ } while(0)
+/* End of bond matrix macros */
+
+
+/*
+ Construction of bond matrix, and its derivatives
+ with respect to the coordinates
+*/
+void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
+ double M [8][8],double Mx[8][8],
+ double My[8][8],double Mz[8][8],
+ double *fl_deriv_sum_p) {
+
+ const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r;
+ const double x = xin*ri,y = yin*ri,z = zin*ri;
+
+ // d-d
+ // call delndd(x,y,z)
+ const double x2 = x*x,y2 = y*y,z2 = z*z;
+ const double xy = x*y,xz = x*z,yz = y*z;
+
+ const double sr3 = sqrt(3.0),sr3i = 1.0/sr3;
+ const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0;
+
+ const double ddl_1 = ddl[1],ddl_2 = ddl[2],ddl_3 = ddl[3];
+ const double w4 = ddl_1 - frac_4_3*ddl_2 + frac_1_3*ddl_3;
+ const double w2 = ddl_2 - ddl_3;
+ const double w0 = ddl_2;
+
+
+ //del4
+ double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5;
+ double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x;
+ double gsl_1y,gsl_2y,gsl_3y,gsl_4y,gsl_5y;
+ double gsl_1z,gsl_2z,gsl_3z,gsl_4z,gsl_5z;
+
+ double dl2,dl2x,dl2y,dl2z;
+
+ double fl,fl_x,fl_y,fl_z,fl_ri;
+ double fl_rp,fl_p1,fl_r0,fl_al;
+
+ gsl_1 = 0.5*(3.0*z2 - 1.0);
+ gsl_1x = 0.0;
+ gsl_1y = 0.0;
+ gsl_1z = 3.0*z;
+
+ gsl_2 = sr3*xz;
+ gsl_2x = sr3*z;
+ gsl_2y = 0.0;
+ gsl_2z = sr3*x;
+
+ gsl_3 = sr3*yz;
+ gsl_3x = 0.0;
+ gsl_3y = sr3*z;
+ gsl_3z = sr3*y;
+
+ gsl_4 = sr3*(x2 - y2)*0.5;
+ gsl_4x = sr3*x;
+ gsl_4y = -sr3*y;
+ gsl_4z = 0.0;
+
+ gsl_5 = sr3*xy;
+ gsl_5x = sr3*y;
+ gsl_5y = sr3*x;
+ gsl_5z = 0.0;
+
+ // Compute bond length potential
+ fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al);
+ fl_ri = fl*ri;
+
+ *fl_deriv_sum_p =
+ fl_rp*splinepot.drp + fl_p1*splinepot.dp1 +
+ fl_r0*splinepot.dr00 + fl_al*splinepot.dal;
+
+ // del2
+
+ //del2.m[1][1] = z2 - 2.0/3.0;
+ dl2 = z2 - frac_2_3;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 2*z;
+ MAKE_ELEMENT_5(1,1);
+
+ //del2.m[1][2] = xz/sr3;
+ dl2 = xz*sr3i;
+ dl2x = z*sr3i;
+ dl2y = 0.0;
+ dl2z = x*sr3i;
+ MAKE_ELEMENT_5(1,2);
+
+ //del2.m[1][3] = yz/sr3;
+ dl2 = yz*sr3i;
+ dl2x = 0.0;
+ dl2y = z*sr3i;
+ dl2z = y*sr3i;
+ MAKE_ELEMENT_5(1,3);
+
+ //del2.m[1][4] = -(x2 - y2)*sr3i;
+ dl2 = -(x2 - y2)*sr3i;
+ dl2x = -2.0*sr3i*x;
+ dl2y = 2.0*sr3i*y;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(1,4);
+
+ //del2.m[1][5] = -2.0*xy*sr3i;
+ dl2 = -2.0*xy*sr3i;
+ dl2x = -2.0*y*sr3i;
+ dl2y = -2.0*x*sr3i;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(1,5);
+
+ //del2.m[2][2] = -y2;
+ dl2 = -y2;
+ dl2x = 0.0;
+ dl2y = -2.0*y;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(2,2);
+
+ //del2.m[2][3] = xy;
+ dl2 = xy;
+ dl2x = y;
+ dl2y = x;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(2,3);
+
+ //del2.m[2][4] = xz;
+ dl2 = xz;
+ dl2x = z;
+ dl2y = 0.0;
+ dl2z = x;
+ MAKE_ELEMENT_5(2,4);
+
+ //del2.m[2][5] = yz;
+ dl2 = yz;
+ dl2x = 0.0;
+ dl2y = z;
+ dl2z = y;
+ MAKE_ELEMENT_5(2,5);
+
+ //del2.m[3][3] = -x2;
+ dl2 = -x2;
+ dl2x = -2.0*x;
+ dl2y = 0.0;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(3,3);
+
+ //del2.m[3][4] = -yz;
+ dl2 = -yz;
+ dl2x = 0.0;
+ dl2y = -z;
+ dl2z = -y;
+ MAKE_ELEMENT_5(3,4);
+
+ //del2.m[3][5] = xz;
+ dl2 = xz;
+ dl2x = z;
+ dl2y = 0.0;
+ dl2z = x;
+ MAKE_ELEMENT_5(3,5);
+
+ //del2.m[4][4] = -z2;
+ dl2 = -z2;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = -2.0*z;
+ MAKE_ELEMENT_5(4,4);
+
+ //del2.m[4][5] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+ MAKE_ELEMENT_5(4,5);
+
+ //del2.m[5][5] = -z2;
+ dl2 = -z2;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = -2.0*z;
+ MAKE_ELEMENT_5(5,5);
+}
+
+
+void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
+ double M [8][8],double Mx[8][8],
+ double My[8][8],double Mz[8][8],
+ double *fl_deriv_sum_p) {
+
+ const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r;
+ const double x = xin*ri,y = yin*ri,z = zin*ri;
+
+ // d-d
+ // call delndd(x,y,z)
+ const double x2 = x*x,y2 = y*y,z2 = z*z;
+ const double xy = x*y,xz = x*z,yz = y*z;
+ const double x4 = x2*x2,y4 = y2*y2;
+
+ //const double sr3 = sqrt(3.0);//,sr3i = 1.0/sr3;
+ //const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0;
+
+ const double sr01 = sqrt(0.1);
+ const double sr015 = sqrt(0.15);
+ const double sr024 = sqrt(0.24);
+ const double sr0375 = sqrt(0.375);
+ const double sr06 = sqrt(0.6);
+ const double sr0625 = sqrt(0.625);
+ const double sr09 = sqrt(0.9);
+ const double sr15 = sqrt(1.5);
+ const double sr24 = sqrt(2.4);
+ const double sr36 = sqrt(3.6);
+ const double sr375 = sqrt(3.75);
+ const double sr96 = sqrt(9.6);
+ const double sr150 = sqrt(15.0);
+
+
+
+ const double ddl_1 = ddl[1],ddl_2 = ddl[2],ddl_3 = ddl[3],ddl_4 = ddl[4];
+ const double w6 = ddl_1 - 1.5*ddl_2 + 0.6*ddl_3 - 0.1*ddl_4;
+ const double w4 = 0.625*ddl_2 - ddl_3 + 0.375*ddl_4;
+ const double w2 = 0.625*(ddl_2 - ddl_4);
+ const double w0 = 0.625*ddl_2 + 0.375*ddl_4;
+
+
+ //del6
+ double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5 ,gsl_6, gsl_7;
+ double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x,gsl_6x,gsl_7x;
+ double gsl_1y,gsl_2y,gsl_3y,gsl_4y,gsl_5y,gsl_6y,gsl_7y;
+ double gsl_1z,gsl_2z,gsl_3z,gsl_4z,gsl_5z,gsl_6z,gsl_7z;
+
+ double dl2,dl2x,dl2y,dl2z;
+ double dl4,dl4x,dl4y,dl4z;
+ double t1;
+
+ double fl,fl_x,fl_y,fl_z,fl_ri;
+ double fl_rp,fl_p1,fl_r0,fl_al;
+
+ //gslf[1] = 0.5*(5.0*n2 - 3.0)*n;
+ gsl_1 = 0.5*(5.0*z2 - 3.0)*z;
+ gsl_1x = 0.0;
+ gsl_1y = 0.0;
+ gsl_1z = 7.5*z2 - 1.5;
+
+ //gslf[2] = sr0375*(5.0*n2 - 1.0)*l;
+ gsl_2 = sr0375*(5.0*z2 - 1.0)*x;
+ gsl_2x = sr0375*(5.0*z2 - 1.0);
+ gsl_2y = 0.0;
+ gsl_2z = sr0375*10.0*xz;
+
+ //gslf[3] = sr0375*(5.0*n2 - 1.0)*m;
+ gsl_3 = sr0375*(5.0*z2 - 1.0)*y;
+ gsl_3x = 0.0;
+ gsl_3y = sr0375*(5.0*z2 - 1.0);
+ gsl_3z = sr0375*10.0*yz;
+
+ //gslf[4] = sr375*(l2 - m2)*n;
+ gsl_4 = sr375*(x2 - y2)*z;
+ gsl_4x = 2.0*sr375*xz;
+ gsl_4y = -2.0*sr375*yz;
+ gsl_4z = sr375*(x2 - y2);
+
+ //gslf[5] = sr150*lm*n;
+ gsl_5 = sr150*xy*z;
+ gsl_5x = sr150*yz;
+ gsl_5y = sr150*xz;
+ gsl_5z = sr150*xy;
+
+ //gslf[6] = sr0625*(l2 - 3.0*m2)*l;
+ gsl_6 = sr0625*(x2 - 3.0*y2)*x;
+ gsl_6x = 3.0*sr0625*(x2 - y2);
+ gsl_6y = -6.0*sr0625*xy;
+ gsl_6z = 0.0;
+
+ //gslf[7] = sr0625*(3.0*l2 - m2)*m;
+ gsl_7 = sr0625*(3.0*x2 - y2)*y;
+ gsl_7x = 6.0*sr0625*xy;
+ gsl_7y = 3.0*sr0625*(x2 - y2);
+ gsl_7z = 0.0;
+
+
+ // Compute bond length potential
+ fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al);
+ fl_ri = fl*ri;
+
+ *fl_deriv_sum_p =
+ fl_rp*splinepot.drp + fl_p1*splinepot.dp1 +
+ fl_r0*splinepot.dr00 + fl_al*splinepot.dal;
+
+ // del2f
+
+ //del2f.m[1][1] = 0.4*(3.0*n2 - 1.0);
+ dl2 = 0.4*(3.0*z2 - 1.0);
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 2.4*z;
+
+ //del4f.m[1][1] = 0.60*(5.0*n2 - 4.0)*n2;
+ dl4 = 0.60*(5.0*z2 - 4.0)*z2;
+ dl4x = 0.0;
+ dl4y = 0.0;
+ dl4z = 0.60*(20.0*z2 - 8.0)*z;
+
+ MAKE_ELEMENT_7(1,1);
+
+
+ //del2f.m[1][2] = sr024*ln;
+ dl2 = sr024*xz;
+ dl2x = sr024*z;
+ dl2y = 0.0;
+ dl2z = sr024*x;
+
+ //del4f.m[1][2] = sr024*(5.0*n2 - 2.0)*ln;
+ dl4 = sr024*(5.0*z2 - 2.0)*xz;
+ dl4x = sr024*(5.0*z2 - 2.0)*z;
+ dl4y = 0.0;
+ dl4z = sr024*(15.0*z2 - 2.0)*x;
+
+ MAKE_ELEMENT_7(1,2);
+
+
+ //del2f.m[1][3] = sr024*mn;
+ dl2 = sr024*yz;
+ dl2x = 0.0;
+ dl2y = sr024*z;
+ dl2z = sr024*y;
+
+ //del4f.m[1][3] = sr024*(5.0*n2 - 2.0)*mn;
+ dl4 = sr024*(5.0*z2 - 2.0)*yz;
+ dl4x = 0.0;
+ dl4y = sr024*(5.0*z2 - 2.0)*z;
+ dl4z = sr024*(15.0*z2 - 2.0)*y;
+
+ MAKE_ELEMENT_7(1,3);
+
+
+ //del2f.m[1][4] = -sr06*(l2 - m2);
+ dl2 = -sr06*(x2 - y2);
+ dl2x = -2.0*sr06*x;
+ dl2y = 2.0*sr06*y;
+ dl2z = 0.0;
+
+ //del4f.m[1][4] = -sr06*(l2 - m2)*n2;
+ dl4 = -sr06*(x2 - y2)*z2;
+ dl4x = -2.0*sr06*x*z2;
+ dl4y = 2.0*sr06*y*z2;
+ dl4z = -2.0*sr06*(x2 - y2)*z;
+
+ MAKE_ELEMENT_7(1,4);
+
+
+ //del2f.m[1][5] = -sr24*lm;
+ dl2 = -sr24*xy;
+ dl2x = -sr24*y;
+ dl2y = -sr24*x;
+ dl2z = 0.0;
+
+ //del4f.m[1][5] = -sr24*lm*n2;
+ dl4 = -sr24*xy*z2;
+ dl4x = -sr24*y*z2;
+ dl4y = -sr24*x*z2;
+ dl4z = -2.0*sr24*xy*z;
+
+ MAKE_ELEMENT_7(1,5);
+
+
+ //del2f.m[1][6] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[1][6] = sr36*(3.0*m2 - l2)*ln;
+ dl4 = sr36*(3.0*y2 - x2)*xz;
+ dl4x = 3.0*sr36*(y2 - x2)*z;
+ dl4y = 6.0*sr36*y*xz;
+ dl4z = sr36*(3.0*y2 - x2)*x;
+
+ MAKE_ELEMENT_7(1,6);
+
+
+ //del2f.m[1][7] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[1][7] = -sr36*(3.0*l2 - m2)*mn;
+ dl4 = -sr36*(3.0*x2 - y2)*yz;
+ dl4x = -6.0*sr36*x*yz;
+ dl4y = -3.0*sr36*(x2 - y2)*z;
+ dl4z = -sr36*(3.0*x2 - y2)*y;
+
+ MAKE_ELEMENT_7(1,7);
+
+
+ //del2f.m[2][2] = 0.3*(1.0 - 4.0*m2 + n2);
+ dl2 = 0.3 - 1.2*y2 + 0.3*z2;
+ dl2x = 0.0;
+ dl2y = -2.4*y;
+ dl2z = 0.6*z;
+
+ //del4f.m[2][2] = -0.4*l*l - 2.5*(m2 - 0.6*l2)*n2;
+ dl4 = -0.4*x2 - 2.5*(y2 - 0.6*x2)*z2;
+ dl4x = -0.8*x + 3.0*x*z2;
+ dl4y = -5.0*y*z2;
+ dl4z = -5.0*(y2 - 0.6*x2)*z;
+
+ MAKE_ELEMENT_7(2,2);
+
+
+ //del2f.m[2][3] = 1.2*lm;
+ dl2 = 1.2*xy;
+ dl2x = 1.2*y;
+ dl2y = 1.2*x;
+ dl2z = 0.0;
+
+ //del4f.m[2][3] = 0.4*(10.0*n2 - 1.0)*lm;
+ dl4 = (4.0*z2 - 0.4)*xy;
+ dl4x = (4.0*z2 - 0.4)*y;
+ dl4y = (4.0*z2 - 0.4)*x;
+ dl4z = 8.0*z*xy;
+
+ MAKE_ELEMENT_7(2,3);
+
+
+ //del2f.m[2][4] = sr09*ln;
+ dl2 = sr09*xz;
+ dl2x = sr09*z;
+ dl2y = 0.0;
+ dl2z = sr09*x;
+
+ //del4f.m[2][4] = sr01*(6.0*n2 - 8.0*m2 - 1.0)*ln;
+ dl4 = sr01*(6.0*z2 - 8.0*y2 - 1.0)*xz;
+ dl4x = sr01*(6.0*z2 - 8.0*y2 - 1.0)*z;
+ dl4y = -16.0*sr01*y*xz;
+ dl4z = sr01*(18.0*z2 - 8.0*y2 - 1.0)*x;
+
+ MAKE_ELEMENT_7(2,4);
+
+
+ //del2f.m[2][5] = sr09*mn;
+ dl2 = sr09*yz;
+ dl2x = 0.0;
+ dl2y = sr09*z;
+ dl2z = sr09*y;
+
+ //del4f.m[2][5] = sr01*(2.0*n2 - 8.0*m2 + 3.0)*mn;
+ dl4 = sr01*(2.0*z2 - 8.0*y2 + 3.0)*yz;
+ dl4x = 0.0;
+ dl4y = sr01*(2.0*z2 - 24.0*y2 + 3.0)*z;
+ dl4z = sr01*(6.0*z2 - 8.0*y2 + 3.0)*y;
+
+ MAKE_ELEMENT_7(2,5);
+
+
+ //del2f.m[2][6] = -sr015*(l2 - m2);
+ dl2 = -sr015*(x2 - y2);
+ dl2x = -2.0*sr015*x;
+ dl2y = 2.0*sr015*y;
+ dl2z = 0.0;
+
+ //del4f.m[2][6] = sr375*(l2 - m2 - 1.4*l4 + 1.2*l2*m2 + m4);
+ dl4 = sr375*(x2 - y2 - 1.4*x4 + 1.2*x2*y2 + y4);
+ dl4x = sr375*(2.0 - 5.6*x2 + 2.4*y2)*x;
+ dl4y = sr375*(-2.0 + 2.4*x2 + 4.0*y2)*y;
+ dl4z = 0.0;
+
+ MAKE_ELEMENT_7(2,6);
+
+
+ //del2f.m[2][7] = -sr06*lm;
+ dl2 = -sr06*xy;
+ dl2x = -sr06*y;
+ dl2y = -sr06*x;
+ dl2z = 0.0;
+
+ //del4f.m[2][7] = sr96*(n2 - l2 + 0.25)*lm;
+ dl4 = sr96*(z2 - x2 + 0.25)*xy;
+ dl4x = sr96*(z2 - 3.0*x2 + 0.25)*y;
+ dl4y = sr96*(z2 - x2 + 0.25)*x;
+ dl4z = 2.0*sr96*z*xy;
+
+ MAKE_ELEMENT_7(2,7);
+
+
+ //del2f.m[3][3] = 0.30*(1.0 - 4.0*l2 + n2);
+ dl2 = 0.3 - 1.2*x2 + 0.3*z2;
+ dl2x = -2.4*x;
+ dl2y = 0.0;
+ dl2z = 0.6*z;
+
+ //del4f.m[3][3] = -0.4*m2 - 2.5*(l2 - 0.6*m2)*n2;
+ dl4 = -0.4*y2 - 2.5*(x2 - 0.6*y2)*z2;
+ dl4x = -5.0*x*z2;
+ dl4y = y*(3.0*z2 - 0.8);
+ dl4z = -5.0*(x2 - 0.6*y2)*z;
+
+ MAKE_ELEMENT_7(3,3);
+
+
+ //del2f.m[3][4] = -sr09*mn;
+ dl2 = -sr09*yz;
+ dl2x = 0.0;
+ dl2y = -sr09*z;
+ dl2z = -sr09*y;
+
+ //del4f.m[3][4] = -sr01*(6.0*n2 - 8.0*l2 - 1.0)*mn;
+ dl4 = -sr01*(6.0*z2 - 8.0*x2 - 1.0)*yz;
+ dl4x = 16.0*sr01*x*yz;
+ dl4y = -sr01*(6.0*z2 - 8.0*x2 - 1.0)*z;
+ dl4z = -sr01*(18.0*z2 - 8.0*x2 - 1.0)*y;
+
+ MAKE_ELEMENT_7(3,4);
+
+
+ //del2f.m[3][5] = sr09*ln;
+ dl2 = sr09*xz;
+ dl2x = sr09*z;
+ dl2y = 0.0;
+ dl2z = sr09*x;
+
+ //del4f.m[3][5] = sr01*(2.0*n2 - 8.0*l2 + 3.0)*ln;
+ dl4 = sr01*(2.0*z2 - 8.0*x2 + 3.0)*xz;
+ dl4x = sr01*(2.0*z2 - 24.0*x2 + 3.0)*z;
+ dl4y = 0.0;
+ dl4z = sr01*(6.0*z2 - 8.0*x2 + 3.0)*x;
+
+ MAKE_ELEMENT_7(3,5);
+
+
+ //del2f.m[3][6] = sr06*lm;
+ dl2 = sr06*xy;
+ dl2x = sr06*y;
+ dl2y = sr06*x;
+ dl2z = 0.0;
+
+ //del4f.m[3][6] = sr96*(m2 - n2 - 0.25)*lm;
+ dl4 = sr96*(y2 - z2 - 0.25)*xy;
+ dl4x = sr96*(y2 - z2 - 0.25)*y;
+ dl4y = sr96*(3.0*y2 - z2 - 0.25)*x;
+ dl4z = -2.0*sr96*z*xy;
+
+ MAKE_ELEMENT_7(3,6);
+
+
+ //del2f.m[3][7] = -sr015*(l2 - m2);
+ dl2 = -sr015*(x2 - y2);
+ dl2x = -2.0*sr015*x;
+ dl2y = 2.0*sr015*y;
+ dl2z = 0.0;
+
+ //del4f.m[3][7] = sr375*(l2 - m2 + 1.4*m4 - 1.2*l2*m2 - l4);
+ dl4 = sr375*(x2 - y2 + 1.4*y4 - 1.2*x2*y2 - x4);
+ dl4x = sr375*(2.0 - 2.4*y2 - 4.0*x2)*x;
+ dl4y = sr375*(-2.0 + 5.6*y2 - 2.4*x2)*y;
+ dl4z = 0.0;
+
+ MAKE_ELEMENT_7(3,7);
+
+
+ //del2f.m[4][4] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[4][4] = (2.0 - 3.0*n2)*n2 - 4.0*l2*m2;
+ dl4 = (2.0 - 3.0*z2)*z2 - 4.0*x2*y2;
+ dl4x = -8.0*x*y2;
+ dl4y = -8.0*x2*y;
+ dl4z = (4.0 - 12.0*z2)*z;
+
+ MAKE_ELEMENT_7(4,4);
+
+ //del2f.m[4][5] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[4][5] = 2.0*(l2 - m2)*lm;
+ dl4 = 2.0*(x2 - y2)*xy;
+ dl4x = 2.0*(3.0*x2 - y2)*y;
+ dl4y = 2.0*(x2 - 3.0*y2)*x;
+ dl4z = 0.0;
+
+ MAKE_ELEMENT_7(4,5);
+
+
+ //del2f.m[4][6] = sr15*ln;
+ dl2 = sr15*xz;
+ dl2x = sr15*z;
+ dl2y = 0.0;
+ dl2z = sr15*x;
+
+ //del4f.m[4][6] = -sr15*(2.0*n2 - 1.0)*ln;
+ dl4 = -sr15*(2.0*z2 - 1.0)*xz;
+ dl4x = -sr15*(2.0*z2 - 1.0)*z;
+ dl4y = 0.0;
+ dl4z = -sr15*(6.0*z2 - 1.0)*x;
+
+ MAKE_ELEMENT_7(4,6);
+
+
+ //del2f.m[4][7] = sr15*mn;
+ dl2 = sr15*yz;
+ dl2x = 0.0;
+ dl2y = sr15*z;
+ dl2z = sr15*y;
+
+ //del4f.m[4][7] = -sr15*(2.0*n2 - 1.0)*mn;
+ dl4 = -sr15*(2.0*z2 - 1.0)*yz;
+ dl4x = 0.0;
+ dl4y = -sr15*(2.0*z2 - 1.0)*z;
+ dl4z = -sr15*(6.0*z2 - 1.0)*y;
+
+ MAKE_ELEMENT_7(4,7);
+
+
+ //del2f.m[5][5] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[5][5] = -pow((2.0*n2 - 1.0),2) + 4.0*l2*m2;
+ t1 = 2.0*z2 - 1.0;
+ dl4 = -t1*t1 + 4.0*x2*y2;
+ dl4x = 8.0*x*y2;
+ dl4y = 8.0*x2*y;
+ dl4z = -8.0*t1*z;
+
+ MAKE_ELEMENT_7(5,5);
+
+
+ //del2f.m[5][6] = -sr15*mn;
+ dl2 = -sr15*yz;
+ dl2x = 0.0;
+ dl2y = -sr15*z;
+ dl2z = -sr15*y;
+
+ //del4f.m[5][6] = sr15*(2.0*n2 - 1.0)*mn;
+ dl4 = sr15*(2.0*z2 - 1.0)*yz;
+ dl4x = 0.0;
+ dl4y = sr15*(2.0*z2 - 1.0)*z;
+ dl4z = sr15*(6.0*z2 - 1.0)*y;
+
+ MAKE_ELEMENT_7(5,6);
+
+ //del2f.m[5][7] = sr15*ln;
+ dl2 = sr15*xz;
+ dl2x = sr15*z;
+ dl2y = 0.0;
+ dl2z = sr15*x;
+
+ //del4f.m[5][7] = -sr15*(2.0*n2 - 1.0)*ln;
+ dl4 = -sr15*(2.0*z2 - 1.0)*xz;
+ dl4x = -sr15*(2.0*z2 - 1.0)*z;
+ dl4y = 0.0;
+ dl4z = -sr15*(6.0*z2 - 1.0)*x;
+
+ MAKE_ELEMENT_7(5,7);
+
+
+ //del2f.m[6][6] = -(3.0*n2 - 1.0)/2.0;
+ dl2 = 0.5 - 1.5*z2;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = -3.0*z;
+
+ //del4f.m[6][6] = 1.5*(n2 - 1.0)*n2;
+ dl4 = (1.5*z2 - 1.5)*z2;
+ dl4x = 0.0;
+ dl4y = 0.0;
+ dl4z = (6.0*z2 - 3.0)*z;
+
+ MAKE_ELEMENT_7(6,6);
+
+
+ //del2f.m[6][7] = 0.0;
+ dl2 = 0.0;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = 0.0;
+
+ //del4f.m[6][7] = 0.0;
+ dl4 = 0.0;
+ dl4x = 0.0;
+ dl4y = 0.0;
+ dl4z = 0.0;
+
+ MAKE_ELEMENT_7(6,7);
+
+
+ //del2f.m[7][7] = -(3.0*n2 - 1.0)/2.0;
+ dl2 = 0.5 - 1.5*z2;
+ dl2x = 0.0;
+ dl2y = 0.0;
+ dl2z = -3.0*z;
+
+ //del4f.m[7][7] = 1.5*(n2 - 1.0)*n2;
+ dl4 = (1.5*z2 - 1.5)*z2;
+ dl4x = 0.0;
+ dl4y = 0.0;
+ dl4z = (6.0*z2 - 3.0)*z;
+
+ MAKE_ELEMENT_7(7,7);
+}
+
+/************************************************************************/
+
+/* ----------------------------------------------------------------------
+ * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
+ * potential routine.
+ *
+ * Copyright (2015) Lawrence Livermore National Security, LLC.
+ * Produced at the Lawrence Livermore National Laboratory.
+ * Written by Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty
+ * (moriarty2@llnl.gov)
+ * LLNL-CODE-674031 All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License (as published by the
+ * Free Software Foundation) version 2, dated June 1991.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
+ * GNU General Public License for more details.
+ *
+ * LLNL Preamble Notice
+ * A. This notice is required to be provided under our contract with the
+ * U.S. Department of Energy (DOE). This work was performed under the auspices
+ * of the DOE by Lawrence Livermore National Laboratory under Contract No.
+ * DE-AC52-07NA27344.
+ *
+ * B. Neither the United States Government nor Lawrence Livermore National
+ * Security, LLC nor any of their employees, makes any warranty, express or
+ * implied, or assumes any liability or responsibility for the accuracy,
+ * completeness, or usefulness of any information, apparatus, product, or
+ * process disclosed, or represents that its use would not infringe
+ * privately-owned rights.
+ *
+ * C. Also, reference herein to any specific commercial products, process,
+ * or services by trade name, trademark, manufacturer or otherwise does not
+ * necessarily constitute or imply its endorsement, recommendation, or
+ * favoring by the United States Government or Lawrence Livermore National
+ * Security, LLC. The views and opinions of authors expressed herein do not
+ * necessarily state or reflect those of the United States Government or
+ * Lawrence Livermore National Security, LLC, and shall not be used for
+ * advertising or product endorsement purposes.
+------------------------------------------------------------------------- */
diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h
new file mode 100644
index 000000000..5e5740f39
--- /dev/null
+++ b/src/USER-MGPT/pair_mgpt.h
@@ -0,0 +1,718 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
+ and John Moriarty, LLNL (moriarty2@llnl.gov)
+
+ Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
+ matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted
+ to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski
+ (2011). See LLNL copyright notice at bottom of this file.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(mgpt,PairMGPT)
+
+#else
+
+#ifndef LMP_PAIR_MGPT_H
+#define LMP_PAIR_MGPT_H
+
+#include <new>
+#include <cmath>
+#include <cstdio>
+#include <cassert>
+
+#include "pair.h"
+#include "domain.h"
+
+#include "mgpt_readpot.h"
+#include "mgpt_linalg.h"
+
+
+namespace LAMMPS_NS {
+
+
+class PairMGPT : public Pair {
+ mgpt_linalg linalg;
+public:
+
+ class Doublet {
+ public:
+ int i,j;
+ public:
+ Doublet(const Doublet &t) : i(t.i),j(t.j) {}
+ Doublet(int ii,int jj) : i(ii < jj ? ii:jj),j(ii < jj ? jj : ii) {}
+
+ Doublet operator=(const Doublet &t) {
+ i = t.i;
+ j = t.j;
+ return *this;
+ }
+ int operator==(const Doublet &b) const {
+ return (i == b.i) && (j == b.j);
+ }
+ int hash() const { return i*333331 + j*331; }
+ };
+
+ template<typename T,typename K> class Hash {
+
+ class Link {
+ public:
+ T data;
+ Link *next;
+ K key;
+ int hits;
+ Link(const K &k,Link *n) : next(n),key(k),hits(1) {}
+
+ static void *operator new(std::size_t sz) {
+ const size_t align = 32;
+ size_t x = (size_t) (void *) ::operator new(sz+align);
+ size_t y = (x + align) - ((x+align)&(align-1));
+ assert(sizeof(void *) <= align);
+ assert((x & (sizeof(void *)-1)) == 0);
+ ((void **) y)[-1] = (void *) x;
+ return (void *) y;
+ }
+ static void operator delete(void *ptr) {
+ ::operator delete(((void **) ptr)[-1]);
+ }
+ };
+
+ int isprime(int x) {
+ if(x%2 == 0)
+ return 0;
+ else {
+ int k = 3;
+ while(k*k <= x) {
+ if(x%k == 0) return 0;
+ k = k+2;
+ }
+ return 1;
+ }
+ }
+
+ int size,used;
+ Link **table;
+
+ int maxlength,nstep,nsearch;
+ public:
+
+ class Iterator {
+ Hash &H;
+ int idx;
+ Link *p;
+ public:
+ Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); }
+ Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {}
+ void next() {
+ if(idx >= H.Size()) return;
+ if(p != 0) p = p->next;
+ if(p == 0) {
+ do {
+ idx = idx+1;
+ if(idx >= H.Size()) return;
+ p = H.table[idx];
+ } while(p == 0);
+ }
+ }
+ K *key() { return &p->key; }
+ T *data() { return &p->data; }
+ Link *link() { return p; }
+
+ int operator==(const Iterator &a) {
+ return idx==a.idx && p==a.p;
+ }
+ int operator!=(const Iterator &a) {
+ return !(*this == a);
+ }
+ };
+
+ Hash(int sz) {
+ while(!isprime(sz)) sz = sz + 1;
+ size = sz;
+ used = 0;
+
+
+ table = new Link *[size];
+ for(int i = 0; i<size; i++)
+ table[i] = 0;
+
+ /* Counters for statistics */
+ maxlength = 0;
+ nstep = 0;
+ nsearch = 0;
+ }
+
+ ~Hash() {
+ for(int i = 0; i<size; i++) {
+ Link *p = table[i];
+ while(p != 0) {
+ Link *q = p->next;
+ delete p;
+ p = q;
+ }
+ }
+ delete[] table;
+ }
+
+ Iterator begin() { return Iterator(*this); }
+ Iterator end() { return Iterator(*this,size,0); }
+
+ int Size() { return size; }
+ int Used() { return used; }
+ int NSearch() { return nsearch; }
+ int MaxLength() { return maxlength; }
+ int NStep() { return nstep; }
+ T * Insert(const K &key) {
+ int idx = key.hash() % size;
+ if(idx < 0) idx = idx + size;
+ if(idx >= size || idx < 0) {
+ printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+ exit(1);
+ }
+
+ used = used + 1;
+ if(1) {
+ table[idx] = new Link(key,table[idx]);
+ return &table[idx]->data;
+ } else { /* This is for threading... and incomplete */
+ typedef Link *LinkPtr;
+ LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
+
+ while(ptr != 0) {
+ last = ptr;
+ ptr = ptr->next;
+ }
+ *((volatile LinkPtr *) &(last->next)) = dataptr;
+ return &(dataptr->data);
+ }
+ }
+ void Remove(const K &key) {
+ int idx = key.hash() % size;
+ Link *p,*last = 0;
+ int count = 1;
+ if(idx < 0) idx = idx + size;
+ if(idx >= size || idx < 0) {
+ printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+ exit(1);
+ }
+
+ p = table[idx];
+ while(p != 0 && !(p->key == key)) {
+ last = p;
+ p = p->next;
+ count = count + 1;
+ }
+
+ if(p != 0) {
+ used = used - 1;
+ if(last == 0)
+ table[idx] = p->next;
+ else
+ last->next = p->next;
+ delete p;
+ }
+
+ if(count > maxlength)
+ maxlength = count;
+ nsearch = nsearch + 1;
+ nstep = nstep + count;
+ }
+ T * Lookup(const K &key) {
+ int idx = key.hash() % size;
+ Link *p;
+ int count = 1;
+ if(idx < 0) idx = idx + size;
+ if(idx >= size || idx < 0) {
+ printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+ exit(1);
+ }
+
+
+ p = table[idx];
+ while(p != 0 && !(p->key == key)) {
+ p = p->next;
+ count = count + 1;
+ }
+
+ if(count > maxlength)
+ maxlength = count;
+ nsearch = nsearch + 1;
+ nstep = nstep + count;
+
+ if(p != 0) p->hits++;
+
+ return (p == 0) ? 0 : &p->data;
+ }
+ };
+
+ public:
+ PairMGPT(class LAMMPS *);
+ ~PairMGPT();
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ void init_list(int, class NeighList *);
+ double init_one(int, int);
+
+ private:
+
+ void read_files(const char* parminFile, const char* potinFile, double vol);
+ void allocate();
+
+ struct Matrix {
+ static int sz;
+
+ double m[8][8];
+
+ int align_check() {
+ return ((((unsigned long long int) m) & 31) > 0);
+ }
+ void zero() {
+ for(int i = 0; i<8; i++)
+ for(int j = 0; j<8; j++)
+ m[i][j] = 0.0;
+ }
+
+ void operator=(const Matrix &A) {
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ m[i][j] = A.m[i][j];
+ }
+ void operator=(double x) {
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ m[i][j] = x;
+ }
+ Matrix operator+(const Matrix &B) const {
+ Matrix s;
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ s.m[i][j] = m[i][j] + B.m[i][j];
+ return s;
+ }
+ Matrix operator-(const Matrix &B) const {
+ Matrix s;
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ s.m[i][j] = m[i][j] - B.m[i][j];
+ return s;
+ }
+ Matrix operator-() const {
+ Matrix s;
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ s.m[i][j] = -m[i][j];
+ return s;
+ }
+ Matrix operator*(double x) const {
+ Matrix P;
+ for(int i = 1; i<=sz; i++)
+ for(int j = 0; j<=sz; j++)
+ P.m[i][j] = m[i][j] * x;
+ return P;
+ }
+ Matrix operator/(double x) const {
+ return (*this) * (1.0/x);
+ }
+ Matrix transpose() const {
+ Matrix T;
+ for(int i = 1; i<=sz; i++)
+ for(int j = 1; j<=sz; j++)
+ T.m[j][i] = m[i][j];
+ return T;
+ }
+ };
+ Matrix transpose(const Matrix &A) { return A.transpose(); }
+
+ /* Preprocessor stuff to set alignment requirements on bonda_data
+ and triplet_data structures. Without alignmnt, optimized algebra
+ routines can fail.
+ */
+#ifdef __GNUC__
+ #define PREALIGN struct
+ #define POSTALIGN __attribute__((__aligned__(32)))
+#elif defined(__bgq__)
+ #define PREALIGN __align(32) struct
+ #define POSTALIGN
+#elif defined(__INTEL_COMPILER)
+ /* This will probably not be used, since the Intel compiler also defines __GNUC__ */
+ #define PREALIGN struct __declspec(align(32))
+ #define POSTALIGN
+#else
+ /* Try GNU syntax anyway... */
+ #define PREALIGN struct
+ #define POSTALIGN __attribute__((__aligned__(32)))
+ /*
+ #define PREALIGN struct
+ #define POSTALIGN
+ */
+#endif
+
+ PREALIGN /*struct*/ bond_data {
+ Matrix H,Hx,Hy,Hz;
+ double fl_deriv_sum;
+ double pad[3];
+ } POSTALIGN;
+ PREALIGN /*struct*/ triplet_data {
+ Matrix H1H2;
+ Matrix H1xH2 , H1yH2 , H1zH2;
+ Matrix H1H2x , H1H2y , H1H2z;
+
+ int align_check() {
+ return
+ (H1H2.align_check() << 0) |
+ (H1xH2.align_check() << 1) |
+ (H1yH2.align_check() << 2) |
+ (H1zH2.align_check() << 3) |
+ (H1H2x.align_check() << 4) |
+ (H1H2y.align_check() << 5) |
+ (H1H2z.align_check() << 6) ;
+ }
+
+ void zero() {
+ H1H2.zero();
+ H1xH2.zero(); H1yH2.zero(); H1zH2.zero();
+ H1H2x.zero(); H1H2y.zero(); H1H2z.zero();
+ }
+ } POSTALIGN;
+
+#undef PREALIGN
+#undef POSTALIGN
+
+ void make_bond(const double xx[][3],int i,int j,bond_data *bptr);
+ void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr);
+ triplet_data *get_triplet(const double xx[][3],int i,int j,int k,
+ Hash<bond_data,Doublet> *bhash,triplet_data *twork,
+ double *dvir_ij_p,double *dvir_ik_p);
+
+ int c1_outside(const double a[3],
+ int triclinic,const double alpha[3]) {
+ const double stol = 1e-5;
+
+ if(triclinic) {
+ for(int p = 0; p<3; p++) {
+ double cog = a[p];
+ if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
+ if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
+ }
+
+ } else {
+ double rout = 0.0;
+
+
+ for(int p = 0; p<3; p++) {
+ double cog = a[p];
+ if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
+ if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
+
+ if(cog < domain->sublo[p]-stol) {
+ double t = cog - (domain->sublo[p]-stol);
+ rout = rout + t*t;
+ } else if(cog > domain->subhi[p]+stol) {
+ double t = cog - (domain->subhi[p]+stol);
+ rout = rout + t*t;
+ }
+
+ }
+
+ if(rout > 0.25*rmax*rmax)
+ return 1;
+ }
+
+ return 0;
+ }
+ int c2_outside(const double a[3],const double b[3],
+ int triclinic,const double alpha[3]) {
+ const double stol = 1e-5;
+
+ if(triclinic) {
+ for(int p = 0; p<3; p++) {
+ double cog = 0.5*(a[p] + b[p]);
+ if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
+ if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
+ }
+ } else {
+ double rout = 0.0;
+
+ for(int p = 0; p<3; p++) {
+ double cog = 0.5*(a[p] + b[p]);
+ if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
+ if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
+
+ if(cog < domain->sublo[p]-stol) {
+ double t = cog - (domain->sublo[p]-stol);
+ rout = rout + t*t;
+ } else if(cog > domain->subhi[p]+stol) {
+ double t = cog - (domain->subhi[p]+stol);
+ rout = rout + t*t;
+ }
+
+ }
+
+ if(rout > 0.25*rcrit*rcrit)
+ return 1;
+ }
+
+ return 0;
+ }
+ double get_weight(const int triclinic,
+ const double a[3] = 0,const double b[3] = 0,
+ const double c[3] = 0,const double d[3] = 0) {
+ const double
+ *s0 = triclinic ? domain->sublo_lamda : domain->sublo,
+ *s1 = triclinic ? domain->subhi_lamda : domain->subhi;
+ double weight = 1.0;
+ const double stol = 1e-5;
+
+ for(int p = 0; p<3; p++) {
+ double cog = 0.0,q,w,n = 0.0;
+ if(a != 0) { cog = cog + a[p]; n = n + 1; }
+ if(b != 0) { cog = cog + b[p]; n = n + 1; }
+ if(c != 0) { cog = cog + c[p]; n = n + 1; }
+ if(d != 0) { cog = cog + d[p]; n = n + 1; }
+ cog = cog * (1.0/n);
+
+ if(cog < 0.5*(s0[p]+s1[p])) q = cog - s0[p];
+ else q = s1[p] - cog;
+
+ w = q*(0.5/stol) + 0.5;
+ if(w > 1.0) w = 1.0;
+ if(w < 0.0) w = 0.0;
+ weight = weight * w;
+ }
+ return weight;
+ }
+
+ void force_debug_3t(double xx[][3],
+ int i0,int j0,int k0,
+ int i ,int j ,int k ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz);
+
+ void force_debug_3v(double xx[][3],
+ int i0,int j0,int k0,
+ int i ,int j ,int k ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz);
+
+ void force_debug_4(double xx[][3],
+ int i0,int j0,int k0,int m0,
+ int i ,int j ,int k ,int m ,
+ double dfix,double dfiy,double dfiz,
+ double dfjx,double dfjy,double dfjz,
+ double dfkx,double dfky,double dfkz,
+ double dfmx,double dfmy,double dfmz);
+
+ double numderiv3t(double xx[][3],int i,int j,int k,int p);
+ double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert);
+ double numderiv4(double xx[][3],int i,int j,int k,int m,int p);
+ void compute_x(const int *nnei,const int * const *nlist,
+ double *e_s,double *e_p,double *e_t,double *e_q,
+ int evflag,int newton_pair);
+
+ /* Reimplementation of bond matrix computation */
+ void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
+ double &fl_0,double &fl_x,double &fl_y,double &fl_z,
+ double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
+ void hamltn_5_raw(const double xin,const double yin,const double zin,
+ double M [8][8],double Mx[8][8],
+ double My[8][8],double Mz[8][8],
+ double *fl_deriv_sum_p);
+ void hamltn_7_raw(const double xin,const double yin,const double zin,
+ double M [8][8],double Mx[8][8],
+ double My[8][8],double Mz[8][8],
+ double *fl_deriv_sum_p);
+ /* * */
+ // Old matrix routines, only used in force debug routines.
+
+ /// This function calculates the matrix product of ha and hb.
+ inline Matrix prodmat(const Matrix& ha, const Matrix& hb) const {
+ Matrix h;
+ for(int l = 1; l <= lmax; l++) {
+ for(int n = 1; n <= lmax; n++) {
+ h.m[l][n] = 0.0;
+ for(int m = 1; m <= lmax; m++)
+ h.m[l][n] += ha.m[l][m] * hb.m[m][n];
+ }
+ }
+ return h;
+ }
+
+ /// This function calculates the trace of the matrix product of ha and hb.
+ inline double trace(const Matrix& ha, const Matrix& hb) const {
+ double zquan = 0.0;
+ for(int n = 1; n <= lmax; n++) {
+ double cquan = 0.0;
+ for(int m = 1; m <= lmax; m++)
+ cquan += ha.m[n][m] * hb.m[m][n];
+ zquan += cquan;
+ }
+ return zquan;
+ }
+ /* * */
+
+ inline void transprod(const Matrix& a,const Matrix& b,Matrix &c) const
+ {
+ int i,j,k;
+
+ if(lmax == 5) {
+ const int n = 5;
+ for(i = 1; i<=n; i++)
+ for(j = 1; j<=n; j++) {
+ double s = 0.0;
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[j][k];
+ c.m[i][j] = s;
+ }
+ } else if(lmax == 7) {
+ const int n = 7;
+ for(i = 1; i<=n; i++)
+ for(j = 1; j<=n; j++) {
+ double s = 0.0;
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[j][k];
+ c.m[i][j] = s;
+ }
+ } else {
+ const int n = lmax;
+ for(i = 1; i<=n; i++)
+ for(j = 1; j<=n; j++) {
+ double s = 0.0;
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[j][k];
+ c.m[i][j] = s;
+ }
+ }
+ }
+
+ inline double transtrace_s(const float (*A)[8],const float (*B)[8]) const {
+ const int n = lmax;
+ double s = 0.0;
+ int i,j;
+
+ for(i = 0; i<n; i++)
+ for(j = 1; j<=n; j++)
+ s = s + A[i][j]*B[i][j];
+ return s;
+ }
+ inline double transtrace(const Matrix& a,const Matrix& b) const
+ {
+ int i,k;
+ double s = 0.0;
+
+ if(linalg.single)
+ return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
+
+ //printf("Calling transtrace... That is shit\n");
+
+ if(lmax == 5) {
+ const int n = 5;
+ for(i = 1; i<=n; i++)
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[i][k];
+ } else if(lmax == 7) {
+ const int n = 7;
+ for(i = 1; i<=n; i++)
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[i][k];
+ } else {
+ const int n = lmax;
+ for(i = 1; i<=n; i++)
+ for(k = 1; k<=n; k++)
+ s = s + a.m[i][k]*b.m[i][k];
+ }
+ return s;
+ }
+
+ double cutoff;
+ //double vpair[601];
+ //double ktan[601];
+ //double dvdvol[601];
+ //double delr;
+ //double rp,p1,al,r0,vc,vd,ve,pc,pd,pe;
+ double rmax;
+ double rcrit;
+ //double evol0, pvol0, pot_input_vol;
+ //double epsr, epsa;
+
+ int thrion;
+ int fourion;
+
+ //int mode;
+ double ddl[5];
+ int lmax, lang;
+ Matrix del0;
+ double anorm3, anorm4;
+
+ // Flag indicating whether volumetric pressure should be used.
+ // Volumetric pressure means that terms emanating from the
+ // derivative of the energy with respect to the potential atomic
+ // volume parameter is included.
+ int volpres_flag,nbody_flag;
+
+ potdata splinepot;
+};
+
+}
+
+#endif
+#endif
+
+/* ----------------------------------------------------------------------
+ * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
+ * potential routine.
+ *
+ * Copyright (2015) Lawrence Livermore National Security, LLC.
+ * Produced at the Lawrence Livermore National Laboratory.
+ * Written by Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty
+ * (moriarty2@llnl.gov)
+ * LLNL-CODE-674031 All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License (as published by the Free
+ * Software Foundation) version 2, dated June 1991.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
+ * GNU General Public License for more details.
+ *
+ * LLNL Preamble Notice
+ * A. This notice is required to be provided under our contract with the
+ * U.S. Department of Energy (DOE). This work was performed under the auspices
+ * of the DOE by Lawrence Livermore National Laboratory under Contract No.
+ * DE-AC52-07NA27344.
+ *
+ * B. Neither the United States Government nor Lawrence Livermore National
+ * Security, LLC nor any of their employees, makes any warranty, express or
+ * implied, or assumes any liability or responsibility for the accuracy,
+ * completeness, or usefulness of any information, apparatus, product, or
+ * process disclosed, or represents that its use would not infringe
+ * privately-owned rights.
+ *
+ * C. Also, reference herein to any specific commercial products, process,
+ * or services by trade name, trademark, manufacturer or otherwise does not
+ * necessarily constitute or imply its endorsement, recommendation, or
+ * favoring by the United States Government or Lawrence Livermore National
+ * Security, LLC. The views and opinions of authors expressed herein do not
+ * necessarily state or reflect those of the United States Government or
+ * Lawrence Livermore National Security, LLC, and shall not be used for
+ * advertising or product endorsement purposes.
+------------------------------------------------------------------------- */
diff --git a/src/USER-SMTBQ/README b/src/USER-SMTBQ/README
new file mode 100644
index 000000000..74b621eef
--- /dev/null
+++ b/src/USER-SMTBQ/README
@@ -0,0 +1,14 @@
+This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
+potential for the description of ionocovalent bonds in oxides.
+
+Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot
+at LAAS-CNRS in France.
+
+Contact emails: lammps@u-bourgogne.fr, nsalles@laas.fr
+
+See the doc page for the pair_style smtbq command to get started.
+
+There are potential files for this potential in the potentials dir.
+
+There are example scripts for using this package in
+examples/USER/smtbq.
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
new file mode 100644
index 000000000..52b431a8c
--- /dev/null
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -0,0 +1,4241 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ The SMTBQ code has been developed with the financial support of CNRS and
+ of the Regional Council of Burgundy (Convention n� 2010-9201AAO037S03129)
+
+ Copyright (2015)
+ Universite de Bourgogne : Nicolas SALLES, Olivier POLITANO
+ Universite de Paris-Sud Orsay : R. Tetot
+ Aalto University (Finland) : E. Maras
+
+ Please cite the related publication:
+ N. Salles, O. Politano, E. Amzallag and R. Tetot,
+ Comput. Mater. Sci., 111 (2016) 181-189
+
+ Contact : lammps@u-bourgogne.fr
+
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of
+ the License, or (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ See the GNU General Public License for more details:
+ <http://www.gnu.org/licenses/>.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_smtbq.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "group.h"
+#include "update.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+
+#include <iostream>
+#include <iomanip>
+#include <string>
+#include <fstream>
+
+//to DELETE
+//#include <time.h>
+//#include <sys/time.h>
+//#include <stdlib.h>
+//#include <stdio.h>
+//to DELETE
+using namespace std;
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define MAXLINE 2048
+#define MAXTOKENS 2048
+#define DELTA 4
+#define PGDELTA 1
+#define MAXNEIGH 24
+#define Pi 4*atan(1)
+
+/* ---------------------------------------------------------------------- */
+
+PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp)
+{
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nproc);
+
+ single_enable = 0;
+ restartinfo = 0;
+ one_coeff = 1;
+
+ nmax = 0;
+ rmin = 0.0;
+ dr = 0.0;
+ ds = 0.0;
+ kmax = 0;
+
+ nelements = 0;
+ elements = NULL;
+ nparams = 0;
+ maxparam = 0;
+ params = NULL;
+ intparams = NULL;
+
+ intype = NULL;
+ coultype = NULL;
+ fafb = NULL;
+ dfafb = NULL;
+ potqn = NULL;
+ dpotqn = NULL;
+ Vself = 0.0;
+ tabsmb = NULL;
+ tabsmr = NULL;
+ dtabsmb = NULL;
+ dtabsmr = NULL;
+
+ sbcov = NULL;
+ coord = NULL;
+ sbmet = NULL;
+ chimet = NULL;
+ ecov = NULL;
+
+ potmad = NULL;
+ potself = NULL;
+ potcov = NULL;
+ qf = NULL;
+ q1 = NULL;
+ q2 = NULL;
+ tab_comm = NULL;
+
+ nvsm = NULL;
+ vsm = NULL;
+ flag_QEq = NULL;
+ nQEqaall = NULL;
+ nQEqcall = NULL;
+ nQEqall = NULL;
+ nteam = 0;
+ cluster = 0;
+
+ Nevery = 0.0;
+ Neverypot = 0.0;
+
+ fct = NULL;
+
+
+ maxpage = 0;
+
+ // set comm size needed by this Pair
+
+ comm_forward = 1;
+ comm_reverse = 1;
+}
+
+/* ----------------------------------------------------------------------
+ check if allocated, since class can be destructed when incomplete
+ ------------------------------------------------------------------------- */
+
+PairSMTBQ::~PairSMTBQ()
+{
+ int i;
+ if (elements) {
+ for ( i = 0; i < nelements; i++) delete [] elements[i];
+
+ for( i = 0; i < atom->ntypes ; i++ ) free( params[i].nom );
+ for( i = 1; i <= maxintparam ; i++ ) free( intparams[i].typepot );
+ for( i = 1; i <= maxintparam ; i++ ) free( intparams[i].mode );
+ }
+
+ free(QEqMode);
+ free(QInitMode);
+ free(writepot);
+ free(writeenerg);
+ free(Bavard);
+
+ delete [] elements;
+ memory->sfree(params);
+ memory->sfree(intparams);
+
+ memory->destroy(intype);
+ memory->destroy(coultype);
+ memory->destroy(fafb);
+ memory->destroy(dfafb);
+ memory->destroy(potqn);
+ memory->destroy(dpotqn);
+
+ memory->destroy(ecov);
+ memory->destroy(sbcov);
+ memory->destroy(coord);
+ memory->destroy(sbmet);
+ memory->destroy(tabsmb);
+ memory->destroy(tabsmr);
+ memory->destroy(dtabsmb);
+ memory->destroy(dtabsmr);
+
+ memory->destroy(potmad);
+ memory->destroy(potself);
+ memory->destroy(potcov);
+ memory->destroy(chimet);
+
+ memory->destroy(nvsm);
+ memory->destroy(vsm);;
+ memory->destroy(flag_QEq);
+
+ memory->destroy(nQEqall);
+ memory->destroy(nQEqcall);
+ memory->destroy(nQEqaall);
+
+ memory->destroy(qf);
+ memory->destroy(q1);
+ memory->destroy(q2);
+ memory->destroy(tab_comm);
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ delete [] map;
+ delete [] esm;
+ }
+
+ memory->destroy(fct);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ map = new int[n+1];
+ esm = new double[n];
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSMTBQ::settings(int narg, char **arg)
+{
+ if (narg > 0) error->all(FLERR,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSMTBQ::coeff(int narg, char **arg)
+{
+ int i,j,n;
+
+ if (!allocated) allocate();
+
+ if (narg != 3 + atom->ntypes)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // insure I,J args are * *
+
+ if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // read args that map atom types to elements in potential file
+ // map[i] = which element the Ith atom type is, -1 if NULL
+ // nelements = # of unique elements
+ // elements = list of element names
+
+ if (elements) {
+ for (i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ }
+ elements = new char*[atom->ntypes];
+ for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
+
+ nelements = 0;
+ for (i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"NULL") == 0) {
+ map[i-2] = -1;
+ continue;
+ }
+ for (j = 0; j < nelements; j++)
+ if (strcmp(arg[i],elements[j]) == 0) break;
+ map[i-2] = j;
+ if (j == nelements) {
+ n = strlen(arg[i]) + 1;
+ elements[j] = new char[n];
+ strcpy(elements[j],arg[i]);
+ nelements++;
+ }
+ }
+
+ // read potential file and initialize potential parameters
+
+ read_file(arg[2]);
+
+ n = atom->ntypes;
+
+ // generate Coulomb 1/r energy look-up table
+
+ if (comm->me == 0 && screen) fprintf(screen,"Pair SMTBQ:\n");
+ if (comm->me == 0 && screen)
+ fprintf(screen," generating Coulomb integral lookup table ...\n");
+
+ tabqeq();
+
+ // ------------
+
+
+ if (comm->me == 0 && screen)
+ fprintf(screen," generating Second Moment integral lookup table ...\n");
+
+ tabsm();
+
+ // ------------
+
+ // clear setflag since coeff() called once with I,J = * *
+
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+
+ // set setflag i,j for type pairs where both are mapped to elements
+
+ int count = 0;
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ if (map[i] >= 0 && map[j] >= 0) {
+ setflag[i][j] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+ ------------------------------------------------------------------------- */
+
+void PairSMTBQ::init_style()
+{
+ if (atom->tag_enable == 0)
+ error->all(FLERR,"Pair style SMTBQ requires atom IDs");
+ if (force->newton_pair == 0)
+ error->all(FLERR,"Pair style SMTBQ requires newton pair on");
+ if (!atom->q_flag)
+ error->all(FLERR,"Pair style SMTBQ requires atom attribute q");
+
+
+ // need a full neighbor list
+
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+
+ pgsize = neighbor->pgsize;
+ oneatom = neighbor->oneatom;
+ // if (maxpage == 0) add_pages();
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSMTBQ::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ return cutmax;
+}
+
+/* ----------------------------------------------------------------------
+ ---------------------------------------------------------------------- */
+
+void PairSMTBQ::read_file(char *file)
+{
+ int c, num_atom_types,i,k,m,test,j,verbose;
+ char **words;
+
+ memory->sfree(params);
+ params = NULL;
+ memory->sfree(intparams);
+ intparams = NULL;
+ nparams = 0;
+ maxparam = 0;
+ maxintparam = 0;
+
+ verbose = 1;
+ verbose = 0;
+
+ // open file on proc 0
+ FILE *fp;
+ fp = fopen( file, "r" );
+ if ( fp == NULL ) {
+ fprintf( stderr, "error opening the force filed file! terminating...\n" );
+ }
+
+
+ // read each line out of file, skipping blank lines or leading '#'
+ // store line of params if all 3 element tags are in element list
+
+ char *ptr;
+
+ ptr = (char*) malloc(sizeof(char)*MAXLINE);
+ words = (char**) malloc(sizeof(char*)*MAXTOKENS);
+ for (i=0; i < MAXTOKENS; i++)
+ words[i] = (char*) malloc(sizeof(char)*MAXTOKENS);
+
+
+ /* strip comment, skip line if blank */
+
+ if (verbose) printf ("\n");
+ fgets(ptr,MAXLINE,fp);
+ while (strchr(ptr,'#')) {
+ if (verbose) printf ("%s",ptr);
+ fgets(ptr,MAXLINE,fp);
+ }
+
+
+ // Nombre d'atome different dans la structure
+ // ===============================================
+ c = Tokenize( ptr, &words );
+ num_atom_types = atoi(words[1]);
+ if (verbose) printf (" %s %d\n", words[0], num_atom_types);
+
+ memory->create(intype,num_atom_types,num_atom_types,"pair:intype");
+
+ m = 0;
+ for (i = 0; i < num_atom_types; i++) {
+ for (j = 0; j < num_atom_types; j++) {
+ if (j < i) { intype[i][j] = intype[j][i];}
+ else { intype[i][j] = 0;
+ m = m + 1; }
+ if (verbose) printf ("i %d, j %d, intype %d - nb pair %d\n",i,j,intype[i][j],m);
+ }
+ }
+
+ // load up parameter settings and error check their values
+
+ if (nparams == maxparam) {
+ maxparam += DELTA;
+ params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
+ "pair:params");
+ maxintparam += m;
+ intparams = (Intparam *) memory->srealloc(intparams,(maxintparam+1)*sizeof(Intparam),
+ "pair:intparams");
+ }
+
+ for (i=0; i < num_atom_types; i++)
+ params[i].nom = (char*) malloc(sizeof(char)*3);
+
+ for (i=1; i <= maxintparam; i++)
+ intparams[i].typepot = (char*) malloc(sizeof(char)*15);
+
+ for (i=1; i <= maxintparam; i++)
+ intparams[i].mode = (char*) malloc(sizeof(char)*6);
+
+ QEqMode = (char*) malloc(sizeof(char)*18);
+ Bavard = (char*) malloc(sizeof(char)*5);
+ QInitMode = (char*) malloc(sizeof(char)*18);
+ writepot = (char*) malloc(sizeof(char)*5);
+ writeenerg = (char*) malloc(sizeof(char)*5);
+
+
+ // Little loop for ion's parameters
+ // ================================================
+ for (i=0; i<num_atom_types; i++) {
+
+ fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
+
+ // Line 2 - Al
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy(params[i].nom , words[1]);
+ params[i].sto = atof(words[2]);
+ if (verbose) printf (" %s %s %f\n", words[0],params[i].nom,params[i].sto);
+
+ //Line 3 - Charges
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ params[i].qform = atof(words[1]);
+ params[i].masse = atof(words[2]);
+ if (verbose) printf (" %s %f %f \n", words[0],params[i].qform, params[i].masse);
+
+ // Line 4 - Parametres QEq
+
+ fgets( ptr, MAXLINE, fp);
+ c=Tokenize ( ptr, &words );
+ params[i].ne = atof(words[1]) ;
+ params[i].chi = atof(words[2]) ;
+ params[i].dj = atof(words[3]) ;
+
+ if(strcmp(params[i].nom,"O")!=0){
+ params[i].R = atof(words[4]) ;
+ if (verbose) printf(" %s %f %f %f %f\n",words[0],params[i].ne,params[i].chi,
+ params[i].dj,params[i].R);
+ } else {
+ if (verbose) printf(" %s %f %f %f\n",words[0],params[i].ne,params[i].chi,params[i].dj);
+ }
+
+
+ // Line 4bis - Coordinance et rayon pour Ox
+ if(strcmp(params[i].nom,"O")==0){
+
+ fgets( ptr, MAXLINE, fp);
+ c=Tokenize ( ptr, &words );
+
+ coordOxBB= atof(words[1]) ;
+ coordOxBulk= atof(words[2]) ;
+ coordOxSurf= atof(words[3]) ;
+ ROxBB = atof(words[4]) ;
+ params[i].R = atof(words[5]) ;
+ ROxSurf = atof(words[6]) ;
+ if (verbose) printf(" %s %f %f %f %f %f %f\n",words[0],coordOxBB,coordOxBulk,coordOxSurf,ROxBB,params[i].R,ROxSurf);
+ }
+
+ // Ligne 5 - Nombre d'etats partages
+
+ fgets( ptr, MAXLINE, fp);
+ c=Tokenize ( ptr, &words );
+ params[i].n0 = atof(words[1]);
+ if (verbose) printf(" %s %f\n",words[0],params[i].n0);
+
+ // Parametres de Slater
+ params[i].dzeta = (2.0*params[i].ne + 1.0)/(4.0*params[i].R);
+ if (verbose) printf (" Parametre dzeta (Slater) : %f\n",params[i].dzeta);
+
+ } // Fin elements i
+
+ /* =====================================================================
+ reading the interaction's parameters
+ ===================================================================== */
+
+ m = 0; maxintsm = 0; //
+ for (k=0 ; k<=maxintparam ; k++){intparams[k].intsm = 0;}
+ // ---------------------------------
+ for (k = 0; k < maxintparam; k++) {
+ // ---------------------------------
+ m += 1;
+
+ // Ligne 5 - parametre des potentiels
+ fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
+
+ // Lecture des protagonistes
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ test = 0;
+ for (i = 0; i <num_atom_types; i++)
+ {
+ if (strcmp(params[i].nom,words[1])==0) break;
+ if (i == num_atom_types - 1) test = 1;
+ }
+ // if (test == 0) printf (" on a %s -> %d = %s\n",words[1],i,params[i].nom);
+
+ for (j = 0; j <num_atom_types; j++)
+ {
+ if (strcmp(params[j].nom,words[2])==0) break;
+ if (j == num_atom_types - 1) test = 1;
+ }
+ // if (test == 0) printf (" on a %s -> %d = %s\n",words[2],j,params[j].nom);
+
+
+ if ( test == 1 ) {
+ if (verbose) printf ("========== fin des interaction ==========\n");
+ break ; }
+
+
+ intype[i][j] = m;
+ intype[j][i] = intype[i][j];
+ strcpy( intparams[m].typepot , words[3] );
+ intparams[m].intsm = 0;
+ if (verbose) printf (" itype %d jtype %d - intype %d\n",i,j,intype[i][j]);
+
+ if (strcmp(intparams[m].typepot,"second_moment") !=0 &&
+ strcmp(intparams[m].typepot,"buck") != 0 &&
+ strcmp(intparams[m].typepot,"buckPlusAttr") != 0) {
+ error->all(FLERR,"the potential other than second_moment or buckingham have not treated here\n");}
+
+
+ // On detemrine le type d'interaction
+ // -----------------------------------
+ if (strcmp(intparams[m].typepot,"second_moment") == 0) {
+ maxintsm += 1;
+ strcpy( intparams[m].mode , words[4] );
+ intparams[m].intsm = maxintsm;
+
+ if (strcmp(intparams[m].mode,"oxide") != 0 &&
+ strcmp(intparams[m].mode,"metal") != 0){
+ error->all(FLERR,"needs mode to second moment interaction : oxide or metal"); }
+
+// if (strcmp(intparams[m].mode,"oxide") == 0)
+// intparams[m].ncov = min((params[i].sto)*(params[i].n0),(params[j].sto)*(params[j].n0));
+
+ if (verbose) printf(" %s %s %s %s %s \n",words[0],words[1],words[2],
+ intparams[m].typepot,intparams[m].mode);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ intparams[m].a = atof(words[1]) ;
+ intparams[m].p = atof(words[2]) ;
+ intparams[m].ksi = atof(words[3]) ;
+ intparams[m].q = atof(words[4]) ;
+ if (verbose) printf (" %s %f %f %f %f\n",words[0],
+ intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q);
+
+ // Ligne 6 - rayon de coupure potentiel SM
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ intparams[m].dc1 = atof(words[1]) ;
+ intparams[m].dc2 = atof(words[2]) ;
+ intparams[m].r0 = atof(words[3]) ;
+
+
+ if (strcmp(intparams[m].mode,"metal") == 0) {
+ if (verbose) printf (" %s %f %f %f\n",words[0],
+ intparams[m].dc1,intparams[m].dc2,intparams[m].r0);
+ } else {
+ if (verbose) printf (" %s %f %f %f\n",words[0],
+ intparams[m].dc1,intparams[m].dc2,intparams[m].r0);
+ }
+
+
+ } else if (strcmp(intparams[m].typepot,"buck") == 0) {
+
+ if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2],
+ intparams[m].typepot);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ;
+ if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck);
+
+ }
+
+ else if (strcmp(intparams[m].typepot,"buckPlusAttr") == 0) {
+
+ if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2],
+ intparams[m].typepot);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ;
+ if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck);
+
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ intparams[m].aOO = atof(words[1]) ; intparams[m].bOO = atof(words[2]) ;
+ intparams[m].r1OO = atof(words[3]) ;intparams[m].r2OO = atof(words[4]) ;
+ if (verbose) printf (" %s %f %f %f %f \n",words[0],intparams[m].aOO,
+ intparams[m].bOO,intparams[m].r1OO,intparams[m].r2OO);
+
+ }
+ if (verbose) printf (" intsm %d \n",intparams[m].intsm);
+
+ } // for maxintparam
+
+
+ /* ====================================================================
+ tables Parameters
+ ==================================================================== */
+
+ // Ligne 9 - rayon de coupure Electrostatique
+ if (test == 0) {
+ fgets(ptr,MAXLINE,fp);
+ if (verbose) printf ("%s\n",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ }
+ c= Tokenize( ptr, &words );
+
+ for (i=0 ; i<num_atom_types; i++) { params[i].cutsq = atof(words[1]); }
+ cutmax = atof(words[1]);
+ if (verbose) printf (" %s %f\n",words[0],params[0].cutsq);
+
+ // Ligne 9 - parametre pour les tableaux
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+
+ rmin = atof(words[1]) ; dr = atof(words[2]);
+ if (verbose) printf (" %s %f %f\n",words[0],rmin,dr);
+
+ kmax = int(cutmax*cutmax/(2.0*dr*rmin));
+ ds = cutmax*cutmax/double(kmax) ;
+ if (verbose) printf (" kmax %d et ds %f\n",kmax,ds);
+
+ /* ======================================================== */
+ fgets( ptr, MAXLINE, fp);
+ if (verbose) printf ("%s",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ Qstep = atoi(words[1]);
+ if (verbose) printf (" %s %d\n",words[0],Qstep);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ loopmax = atoi(words[1]);
+ precision = atof(words[2]);
+ if (verbose) printf (" %s %d %f\n",words[0],loopmax,precision);
+
+ /* Param de coordination ============================================= */
+
+ fgets( ptr, MAXLINE, fp);
+ if (verbose) printf ("%s",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ r1Coord = atof(words[1]);
+ r2Coord = atof(words[2]);
+ if (verbose) printf (" %s %f %f\n",words[0],r1Coord,r2Coord);
+
+
+
+ /* Mode for QInit============================================= */
+ fgets( ptr, MAXLINE, fp);
+ if (verbose) printf ("%s",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy( QInitMode , words[1] );
+ if (strcmp(QInitMode,"true") == 0) { QOxInit= atof(words[2]); }
+ else { QOxInit = 0.0; }
+ if (verbose) printf (" %s %s %f\n",words[0],QInitMode,QOxInit);
+
+
+ /* Mode for QEq============================================= */
+
+ fgets( ptr, MAXLINE, fp);
+ if (verbose) printf ("%s",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy( QEqMode , words[1] );
+ if (verbose) printf (" %s %s\n",words[0],QEqMode);
+
+ fgets( ptr, MAXLINE, fp);
+
+ if (strcmp(QEqMode,"BulkFromSlab") == 0)
+ {
+
+ c= Tokenize( ptr, &words );
+ zlim1QEq = atof(words[1]);
+ zlim2QEq = atof(words[2]);
+ if (verbose) printf (" %s %f %f\n",words[0],zlim1QEq,zlim2QEq);
+
+ }
+ else if (strcmp(QEqMode,"Surface") == 0)
+ {
+ c= Tokenize( ptr, &words );
+ zlim1QEq = atof(words[1]);
+ if (verbose) printf (" %s %f \n",words[0],zlim1QEq);
+
+ }
+ else if (strcmp(QEqMode,"QEqAll") != 0 &&
+ strcmp(QEqMode,"QEqAllParallel") != 0 &&
+ strcmp(QEqMode,"Surface") != 0 )
+ { error->all(FLERR,"The QEq Mode is not known. QEq mode should be :\n Possible QEq modes | parameters\n QEqAll | no parameters\n QEqAllParallel | no parameters\n Surface | zlim (QEq only for z>zlim)\n BulkFromSlab | zlim1 zlim2 (QEq only for zlim1<z<zlim2)\n"); }
+
+ /* Bavard============================================= */
+
+ fgets( ptr, MAXLINE, fp);
+ if (verbose) printf ("%s",ptr);
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy( Bavard , words[1] );
+ if (verbose) printf (" %s %s\n",words[0],Bavard);
+
+// ---------------------------------------
+// Writing the energy component.
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy( writeenerg, words[1] );
+ if (strcmp (writeenerg,"true") == 0) { Nevery = atof(words[2]); }
+ else { Nevery = 0.0; }
+ if (verbose) printf (" %s %s %f\n",words[0],writeenerg,Nevery);
+
+// ---------------------------------------
+// Writing the chimical electronic potential.
+
+ fgets( ptr, MAXLINE, fp);
+ c= Tokenize( ptr, &words );
+ strcpy( writepot, words[1] );
+ if (strcmp (writepot,"true") == 0) { Neverypot = atof(words[2]); }
+ else { Neverypot = 0.0; }
+ if (verbose) printf (" %s %s %f\n",words[0],writepot,Neverypot);
+
+
+ /* ======================================================== */
+
+ /* deallocate helper storage */
+ for( i = 0; i < MAXTOKENS ; i++ ) free( words[i] );
+ free( words );
+ free( ptr );
+
+ fclose(fp);
+
+ // === Rayon de coupure premier voisins : 1,2*r0
+ for (i=0 ; i<num_atom_types ; i++) {
+ for (j=0 ; j<=i ; j++)
+ {
+ m = intype[i][j];
+ if (m == 0) continue;
+ if (intparams[m].intsm == 0) continue;
+
+ intparams[m].neig_cut = 1.2*intparams[m].r0;
+ if (strcmp(intparams[m].typepot,"second_moment") == 0 )
+ if (verbose) printf (" Rc 1er voisin, typepot %s -> %f Ang\n",
+ intparams[m].typepot,intparams[m].neig_cut);
+ }
+ }
+
+ //A adapter au STO
+ ncov = min((params[0].sto)*(params[0].n0),(params[1].sto)*(params[1].n0));
+
+ if (verbose) printf (" Parametre ncov = %f\n",ncov);
+ if (verbose) printf (" ********************************************* \n");
+
+
+
+}
+
+/* ----------------------------------------------------------------------
+ * COMPUTE
+ ---------------------------------------------------------------------- */
+
+void PairSMTBQ::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,m,gp;
+ int itag,jtag,itype,jtype;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+ double rsq,iq,jq,Eself,natom;
+ double ecovtot,ErepOO,ErepMO,Eion,Ecoh;
+ double **tmp,**tmpAll,*nmol;
+ double dq,dqcov;
+
+
+ int bavard;
+
+
+ if (atom->nmax > nmax) {
+ memory->destroy(ecov);
+ memory->destroy(potmad);
+ memory->destroy(potself);
+ memory->destroy(potcov);
+ memory->destroy(sbcov);
+ memory->destroy(coord);
+ memory->destroy(sbmet);
+ memory->destroy(chimet);
+ memory->destroy(flag_QEq);
+ memory->destroy(qf);
+ memory->destroy(q1);
+ memory->destroy(q2);
+ memory->destroy(tab_comm);
+
+ nmax = atom->nmax;
+
+ memory->create(ecov,nmax,"pair:ecov");
+ memory->create(potmad,nmax,"pair:potmad");
+ memory->create(potself,nmax,"pair:potself");
+ memory->create(potcov,nmax,"pair:potcov");
+ memory->create(sbcov,nmax,"pair:sbcov");
+ memory->create(coord,nmax,"pair:coord");
+ memory->create(sbmet,nmax,"pair:sbmet");
+ memory->create(chimet,nmax,"pair:chimet");
+ memory->create(flag_QEq,nmax,"pair:flag_QEq");
+ memory->create(qf,nmax,"pair:qf");
+ memory->create(q1,nmax,"pair:q1");
+ memory->create(q2,nmax,"pair:q2");
+ memory->create(tab_comm,nmax,"pair:tab_comm");
+ }
+
+
+ evdwl = ecoul = ecovtot = ErepOO = ErepMO = Eion = 0.0;
+ Eself = 0.0;
+
+ if (eflag || vflag) { ev_setup(eflag,vflag); }
+ else { evflag = vflag_fdotr = vflag_atom = 0; }
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *tag = atom->tag;
+ int *type = atom->type;
+ int newton_pair = force->newton_pair;
+ int nlocal = atom->nlocal;
+ int step = update->ntimestep;
+ struct timeval start, end;
+
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ if (step == 0 || (Qstep !=0 && fmod(double(step), double(Qstep)) == 0.0 )) Charge();
+// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+// this is necessary to get sbcov or sbmet table in order to caclulate the covalent or metal bonding
+ if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0 ) QForce_charge(0);
+
+
+ // Charges Communication
+ // ----------------------
+ forward(q) ; reverse(q);
+
+ memory->create(nmol,nteam+1,"pair:nmol");
+ memory->create(tmp,nteam+1,7,"pair:tmp");
+ memory->create(tmpAll,nteam+1,7,"pair:tmpAll");
+
+
+ for (i=0; i<nteam+1; i++) {
+ nmol[i] = double(nQEqall[i]);
+ for (j=0; j<7; j++) { tmp[i][j] = 0.0; tmpAll[i][j] = 0.0; }
+ }
+
+
+ /* ------------------------------------------------------------------------
+ Energy component store in tmp[gp][:] with gp is # QEq group
+ 0 -> ionic energy
+ 1 -> coulombian energy
+ 2 -> Electrosatic energy (ionic + Coulombian)
+ 3 -> Short int. Ox-Ox
+ 4 -> Short int. SMTB (repulsion)
+ 5 -> Covalent energy SMTB
+ 6 -> Somme des Q(i)�
+ ------------------------------------------------------------------------- */
+
+ // -----------
+ bavard = 0;
+ // -----------
+
+ /* -------------- N-body forces Calcul --------------- */
+
+ for (ii = 0; ii < inum; ii++) {
+// ===============================
+ i = ilist[ii];
+ itag = tag[i];
+ itype = map[type[i]];
+ iq = q[i];
+ gp = flag_QEq[i];
+
+ if (gp == 0 && itype > 0) natom += 1.0;
+ // if (gp == 0 && itype > 0) nmol[gp] += 1.0;
+
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ // --- For atom i
+ tmp[gp][6] += iq*iq;
+
+
+// self energy, only on i atom
+// ---------------------------
+ Eself = self(¶ms[itype],iq);
+ tmp[gp][0] += Eself;
+ tmp[gp][2] += Eself;
+
+ if (evflag) ev_tally_full (i,0.0,2.0*Eself,0.0,0.0,0.0,0.0);
+
+
+// N-body energy of i
+// ---------------------
+ dq = fabs(params[itype].qform) - fabs(iq);
+ dqcov = dq*(2.0*ncov/params[itype].sto - dq);
+
+ ecov[i] = - sqrt(sbcov[i]*dqcov + sbmet[i]);
+ ecovtot += ecov[i];
+ tmp[gp][5] += ecov[i];
+
+ if (evflag) ev_tally_full(i,0.0,2.0*ecov[i],0.0,0.0,0.0,0.0);
+
+
+// Coulombian Interaction
+// -----------------------
+ evdwl = 2.0*Vself*iq*iq ;
+ tmp[gp][1] += Vself*iq*iq;
+ tmp[gp][2] += Vself*iq*iq;
+
+ if (evflag) ev_tally_full (i,0.0,evdwl,0.0,0.0,0.0,0.0);
+ evdwl = 0.0 ;
+
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+// ===============================
+ j = jlist[jj];
+ jtype = map[type[j]];
+ jtag = tag[j]; jq = q[j];
+
+
+// .......................................................................
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < x[i][2]) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+// .......................................................................
+
+
+ // # of interaction
+ // ----------------
+ m = intype[itype][jtype];
+
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+
+// ---------------------------------
+ if (sqrt(rsq) > cutmax) continue;
+// ---------------------------------
+
+
+ // Coulombian Energy
+ // ------------------
+ evdwl = 0.0 ; fpair = 0.0;
+ potqeq(i,j,iq,jq,rsq,fpair,eflag,evdwl);
+
+ tmp[gp][1] += evdwl;
+ tmp[gp][2] += evdwl;
+
+
+ // Coulombian Force
+ // -----------------
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ evdwl = 0.0; fpair = 0.0 ;
+
+
+
+// ---------------------
+ if (m == 0) continue;
+// ---------------------
+
+// ----------------------------------------------
+ if ( strcmp(intparams[m].typepot,"buck") == 0 ||
+ strcmp(intparams[m].typepot,"buckPlusAttr") ==0 ) {
+// ----------------------------------------------
+
+ evdwl = 0.0; fpair =0.0;
+ rep_OO (&intparams[m],rsq,fpair,eflag,evdwl);
+ ErepOO += evdwl ;
+ tmp[gp][3] += evdwl;
+
+
+ // repulsion is pure two-body, sums up pair repulsive forces
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ evdwl = 0.0; fpair = 0.0 ;
+
+ } // ----------------------------------- Rep O-O
+
+ if (strcmp(intparams[m].typepot,"buckPlusAttr") == 0 ) {
+// ----------------------------------------------
+
+ evdwl = 0.0; fpair =0.0;
+ Attr_OO (&intparams[m],rsq,fpair,eflag,evdwl);
+ ErepOO += evdwl ;
+ tmp[gp][3] += evdwl;
+
+
+ // repulsion is pure two-body, sums up pair repulsive forces
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ evdwl = 0.0; fpair = 0.0 ;
+
+ } // ----------------------------------- Attr O-O
+
+
+// -----------------------------------------------------------------
+ if (strcmp(intparams[m].typepot,"second_moment") != 0 ) continue;
+// -----------------------------------------------------------------
+
+
+ if (sqrt(rsq) > intparams[m].dc2) continue;
+// -------------------------------------------
+
+// Repulsion : Energy + force
+// ----------------------------
+ evdwl = 0.0; fpair = 0.0 ;
+ repulsive(&intparams[m],rsq,i,j,fpair,eflag,evdwl);
+ ErepMO += evdwl;
+ tmp[gp][4] += 2.0*evdwl;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,2.0*evdwl,0.0,fpair,delx,dely,delz);
+
+ evdwl = 0.0 ; fpair = 0.0;
+// ----- ----- ----- ----- ----- -----
+
+// Attraction : force
+// ------------------
+ fpair = 0.0;
+ f_att(&intparams[m], i, j, rsq, fpair) ;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz);
+
+
+ } // --------------------------------- End j
+
+ } // ---------------------------------- End i
+
+
+ if (vflag_fdotr) virial_fdotr_compute();
+
+
+ for (i = 0; i < nteam+1; i++) {
+ MPI_Allreduce(tmp[i],tmpAll[i],7,MPI_DOUBLE,MPI_SUM,world);
+ }
+
+// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+ if (me == 0 && fmod(double(step), Nevery) == 0.0 && strcmp(writeenerg,"true") == 0) {
+
+ ofstream fichierE;
+
+ if (step == 0) { fichierE.open ("Energy_component.txt", ios::out | ios::trunc) ;}
+ else { fichierE.open ("Energy_component.txt", ios::out | ios::app) ;}
+
+ if (fichierE) fichierE<< setprecision(9) <<step;
+
+ for (gp = 0; gp < nteam+1; gp++) {
+ if (nmol[gp] == 0) continue;
+ if (fichierE) fichierE<< setprecision(9) <<" "<<gp<<" "<<nmol[gp]
+ <<" "<<tmpAll[gp][2]<<" "<<tmpAll[gp][3]<<" "<<tmpAll[gp][4]+tmpAll[gp][5];
+ }
+ if (fichierE) fichierE<<endl;
+ if (fichierE) fichierE.close();
+ }
+// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+ if (me == 0&& strcmp(Bavard,"false") != 0) {
+ printf ("A la fin de Compute\n");
+
+ printf ("Nemton_pair : %d, evflag %d, tail_flag %d,vflag_fdotr %d\n",
+ newton_pair,evflag,force->pair->tail_flag,vflag_fdotr);
+ printf ("neighbor->includegroup %d\n",neighbor->includegroup);
+
+
+
+ for (gp=0; gp<nteam+1; gp++) { // -------------------------- Boucle sur les gp
+
+ printf ("Energie de la team %d -- %d atome -------(nteam = %d) \n ",gp,int(nmol[gp]),nteam);
+
+ if (nmol[gp] == 0) {
+ printf (" ============================================ \n \n");
+ continue;
+ }
+ printf ("Vself %f, Som q2 : %f, nmol %f\n",Vself,tmpAll[gp][6],nmol[gp]);
+ // printf ("nmol %f\n",nmol[gp]);
+ printf ("Energie coul tot : %f | %f par mol\n",tmpAll[gp][1],tmpAll[gp][1]/nmol[gp]);
+ printf ("Energie ionique : %f | %f par mol\n",tmpAll[gp][0],tmpAll[gp][0]/nmol[gp]);
+ printf ("Energie elect tot : %f | %f par mol\n",tmpAll[gp][2],tmpAll[gp][2]/nmol[gp]);
+ printf ("Energie cp pair ox : %f | %f par mol\n",tmpAll[gp][3],tmpAll[gp][3]/nmol[gp]);
+ printf ("Energie cp pair sm : %f | %f par mol\n",tmpAll[gp][4],tmpAll[gp][4]/nmol[gp]);
+ printf ("Energie cov sm : %f | %f par mol\n",tmpAll[gp][5],tmpAll[gp][5]/nmol[gp]);
+
+ Ecoh = tmpAll[gp][2] + tmpAll[gp][3] + tmpAll[gp][4] + tmpAll[gp][5];
+ printf ("Energie totale : %f | %f par mol\n",Ecoh,Ecoh/nmol[gp]);
+ printf ("================================================= \n");
+ printf (" \n");
+
+ } // ----------------------------------------------------- Boucle sur les gp
+
+
+
+
+ } // ------------ Call me == 0
+
+ memory->destroy(nmol);
+ memory->destroy(tmp);
+ memory->destroy(tmpAll);
+
+}
+
+/* ----------------------------------------------------------------------
+ Partie Electrostatique
+ ----------------------------------------------------------------------*/
+
+double PairSMTBQ::self(Param *param, double qi)
+{
+ double self_tmp;
+ double s1=param->chi, s2=param->dj;
+
+ self_tmp = qi*(s1+0.5*qi*s2);
+
+ return self_tmp;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSMTBQ::qfo_self(Param *param, double qi)
+{
+ double self_d;
+ double s1 = param->chi;
+ double s2 = param->dj;
+
+ self_d = 0.0 ;
+ self_d = s1+qi*s2;
+
+ return self_d;
+}
+
+/* ---------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::tabqeq()
+{
+ int i,j,k,m,verbose;
+ int nntype;
+ double rc,s,r;
+ double alf;
+
+ int ii;
+ double za,zb,ra,rb,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
+ double aCoeff,bCoeff,rcoupe,nang;
+
+ int n = atom->ntypes;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+ nmax = atom->nmax;
+
+ verbose = 1;
+ verbose = 0;
+
+ nntype = int((n+1)*n/2);
+
+ rc = cutmax ;
+ alf = 0.3 ;
+ // alf = 0.2 ;
+
+
+ if (verbose) printf ("kmax %d, ds %f, nmax %d\n",kmax,ds,nmax);
+ if (verbose) printf ("nlocal = %d, nghost = %d\n",nlocal,nghost);
+ if (verbose) printf ("nntypes %d, kmax %d, rc %f, n %d\n",nntype,kmax,rc,n);
+
+ // allocate arrays
+
+ memory->create(coultype,n,n,"pair:intype");
+ memory->create(potqn,kmax+5,"pair:potqn");
+ memory->create(dpotqn,kmax+5,"pair:dpotqn");
+ memory->create(fafb,kmax+5,nntype,"pair:fafb");
+ memory->create(dfafb,kmax+5,nntype,"pair:dfafb");
+ memory->create(fafbOxOxSurf,kmax+5,"pair:fafbOxOxSurf");
+ memory->create(dfafbOxOxSurf,kmax+5,"pair:dfafbOxOxSurf");
+ memory->create(fafbTiOxSurf,kmax+5,"pair:fafbTiOxSurf");
+ memory->create(dfafbTiOxSurf,kmax+5,"pair:dfafbTiOxSurf");
+
+ memory->create(fafbOxOxBB,kmax+5,"pair:fafbOxOxBB");
+ memory->create(dfafbOxOxBB,kmax+5,"pair:dfafbOxOxBB");
+ memory->create(fafbTiOxBB,kmax+5,"pair:fafbTiOxB");
+ memory->create(dfafbTiOxBB,kmax+5,"pair:dfafbTiOxBB");
+
+
+ memory->create(ecov,nmax,"pair:ecov");
+ memory->create(potmad,nmax,"pair:potmad");
+ memory->create(potself,nmax,"pair:potself");
+ memory->create(potcov,nmax,"pair:potcov");
+ memory->create(sbcov,nmax,"pair:sbcov");
+ memory->create(coord,nmax,"pair:coord");
+ memory->create(sbmet,nmax,"pair:sbmet");
+ memory->create(chimet,nmax,"pair:chimet");
+
+ // memory->create(nvsm,nmax,"pair:nvsm");
+ // memory->create(vsm,nmax,nmax,"pair:vsm");
+ memory->create(flag_QEq,nmax,"pair:flag_QEq");
+
+ memory->create(qf,nmax,"pair:qf");
+ memory->create(q1,nmax,"pair:q1");
+ memory->create(q2,nmax,"pair:q2");
+ memory->create(tab_comm,nmax,"pair:tab_comm");
+
+ memory->create(fct,31,"pair:fct");
+
+ // set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
+
+ m = 0; k = n;
+ for (i = 0; i < n; i++) {
+ for (j = 0; j < n; j++) {
+ if (j == i) {
+ coultype[i][j] = m;
+ m += 1;
+ } else if (j != i && j > i) {
+ coultype[i][j] = k;
+ k += 1;
+ } else if (j != i && j < i) {
+ coultype[i][j] = coultype[j][i];
+ }
+ if (verbose) printf ("i %d, j %d, coultype %d\n",i,j,coultype[i][j]);
+ }
+ }
+
+ // -------- Tabqn --------
+
+ // -------------------
+ // Ouverture du fichier
+ // ofstream fichier("tabqeq.txt", ios::out | ios::trunc) ;
+ // -------------------
+
+ double pi,mu;
+ pi = 4.0*atan(1.0);
+
+ mu = erfc(alf*rc)/rc ;
+
+ //if (fichier) fichier <<" r - potqn " <<endl ;
+
+ //-------------------------
+ for (k=0; k < kmax+5; k++)
+ //-------------------------
+ {
+ s = double(k)*ds ; r = sqrt(s);
+ if (k==0) r=10e-30;
+ potqn[k] = 14.4*(erfc(alf*r)/r - mu) ;
+
+ // $$$ Here is (1/r)*dE/dr
+ dpotqn[k] = -14.4*( (erfc(alf*r)/(r*r) + 2.0*alf/sqrt(pi)/r*exp(-alf*alf*r*r))/r ) ;
+ }
+
+ Vself = -14.4*(alf/sqrt(pi) + mu*0.5) ;
+
+ // --------------------
+ // default arrays to zero
+
+ for (i = 0; i < kmax+5; i ++) {
+ for (j = 0; j < nntype; j ++) {
+ fafb[i][j] = 0.0;
+ dfafb[i][j] = 0.0;
+ }
+ fafbOxOxSurf[i] = 0.0;
+ fafbTiOxSurf[i] = 0.0;
+ dfafbOxOxSurf[i] = 0.0;
+ dfafbTiOxSurf[i] = 0.0;
+
+ fafbOxOxBB[i] = 0.0;
+ fafbTiOxBB[i] = 0.0;
+ dfafbOxOxBB[i] = 0.0;
+ dfafbTiOxBB[i] = 0.0;
+ }
+
+
+ // Set Tabqeq
+ double dij,ddij;
+
+ // -------------------
+ // Ouverture du fichier
+ //ofstream fichier("dtabqeq.txt", ios::out | ios::trunc) ;
+ // -------------------
+
+ //if (fichier) fichier <<" k , r , fafb , dfafb , dfafb2 , dgam , d(1/r) , dpotqn" <<endl ;
+
+
+ rcoupe = cutmax ;
+ double cang ;
+
+ for (i = 0; i < n ; i++){
+ for (j = i; j < n ; j++){
+
+ rc = cutmax; if (verbose) printf ("cutmax %f\n",cutmax);
+ m = coultype[i][j] ;
+ na = params[i].ne ;
+ nb = params[j].ne ;
+ za = params[i].dzeta ;
+ zb = params[j].dzeta ;
+ ra = params[i].R;
+ rb = params[j].R;
+
+ ii = 0 ; nang =cang= 5.0 ;
+ // --------------------------
+ for (k = 0; k < kmax+5; k++)
+ // --------------------------
+ {
+ gam = dgam = dza = dzb = d2zaa = d2zab =
+ d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
+ dij = 0.0 ;
+
+ s = double(k)*ds ; r = sqrt(s) ;
+ if (k==0) r=10e-30;
+
+ gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+
+ // --- Jij
+
+ dij = 14.4 * (1.0/r - double(gam));
+ ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
+
+ // Cutting Fonction
+
+
+ if (dij < 0.01 && ii==0)
+ {
+ ii=2;
+ if (ii==2) if (verbose) printf ("rc : %f\n",r);
+ rc = r ; ii=1 ;
+ if ((rc+nang)>rcoupe) nang = rcoupe - rc ;
+ bCoeff = (2*dij+ddij*nang)/(dij*nang);
+ aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2);
+ }
+ if (r > rc) {dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r);
+ ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r);
+ }
+
+
+ if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
+
+ fafb[k][m] = potqn[k] - dij ;
+ if (k == 1) fafb[0][m] = fafb[k][m] ;
+
+ dfafb[k][m] = dpotqn[k] - ddij/r ;
+ }
+
+ // Make the table fafbOxOxSurf
+ rc = cutmax;
+ if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
+ if(strcmp(params[i].nom,"O")==0) {
+ ra = ROxSurf;
+ za = (2.0*params[i].ne + 1.0)/(4.0*ra);}
+ if(strcmp(params[j].nom,"O")==0) {
+ rb = ROxSurf;
+ zb = (2.0*params[j].ne + 1.0)/(4.0*rb); }
+
+
+ ii = 0 ; nang =cang= 5.0 ;
+ // --------------------------
+ for (k = 0; k < kmax+5; k++)
+ // --------------------------
+ {
+ gam = dgam = dza = dzb = d2zaa = d2zab =
+ d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
+ dij = 0.0 ;
+
+ s = double(k)*ds ; r = sqrt(s) ;
+ if (k==0) r=10e-30;
+
+ gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+
+ // --- Jij
+
+ dij = 14.4 * (1.0/r - double(gam));
+ ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
+
+ if (dij < 0.01 && ii==0)
+ {
+ ii=2;
+ if (ii==2) if (verbose) printf ("rc : %f\n",r);
+ rc = r ; ii=1 ;
+ if ((rc+nang)>rcoupe) nang = rcoupe - rc ;
+ bCoeff = (2*dij+ddij*nang)/(dij*nang);
+ aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2);
+ }
+ if (r > rc) {dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r);
+ ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r);
+ }
+
+
+ if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
+
+ if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
+ fafbOxOxSurf[k] = potqn[k] - dij ;
+ if (k == 1) fafbOxOxSurf[0] = fafbOxOxSurf[k] ;
+
+ dfafbOxOxSurf[k] = dpotqn[k] - ddij/r ;
+ }
+ else { fafbTiOxSurf[k] = potqn[k] - dij ;
+ if (k == 1) fafbTiOxSurf[0] = fafbTiOxSurf[k] ;
+
+ dfafbTiOxSurf[k] = dpotqn[k] - ddij/r ;}
+
+ }
+
+
+ } //for k
+ //end of make the table fafbOxOxSurf
+
+ // Makes the table fafbOxOxBB
+ rc = cutmax;
+ if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
+ if(strcmp(params[i].nom,"O")==0) {
+ ra = ROxBB;
+ za = (2.0*params[i].ne + 1.0)/(4.0*ra);}
+ if(strcmp(params[j].nom,"O")==0) {
+ rb = ROxBB;
+ zb = (2.0*params[j].ne + 1.0)/(4.0*rb); }
+
+
+ ii = 0 ; nang =cang= 5.0 ;
+ // --------------------------
+ for (k = 0; k < kmax+5; k++)
+ // --------------------------
+ {
+ gam = dgam = dza = dzb = d2zaa = d2zab =
+ d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
+ dij = 0.0 ;
+
+ s = double(k)*ds ; r = sqrt(s) ;
+ if (k==0) r=10e-30;
+
+ gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+
+ // --- Jij
+
+ dij = 14.4 * (1.0/r - double(gam));
+ ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
+
+ if (dij < 0.01 && ii==0) {
+ ii=2;
+ if (ii==2) if (verbose) printf ("rc : %f\n",r);
+ rc = r ; ii=1 ;
+ if ((rc+nang)>rcoupe) nang = rcoupe - rc ;
+ bCoeff = (2*dij+ddij*nang)/(dij*nang);
+ aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2);
+ }
+ if (r > rc) {
+ dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r);
+ ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r);
+ }
+
+
+ if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
+
+ if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
+ fafbOxOxBB[k] = potqn[k] - dij ;
+ if (k == 1) fafbOxOxBB[0] = fafbOxOxBB[k] ;
+ dfafbOxOxBB[k] = dpotqn[k] - ddij/r ; }
+ else { fafbTiOxBB[k] = potqn[k] - dij ;
+ if (k == 1) fafbTiOxBB[0] = fafbTiOxBB[k] ;
+ dfafbTiOxBB[k] = dpotqn[k] - ddij/r ;
+ }
+ }
+
+
+
+ } //for k
+ //end of make the table fafbOxOxBB
+
+
+
+ }
+ } //for i,j
+
+ //if (fichier) fichier.close() ;
+
+}
+
+/* ---------------------------------------------------------------------*/
+
+void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
+ double &fforce, int eflag, double &eng)
+{
+
+ /* ===================================================================
+ Coulombian energy calcul between i and j atoms
+ with fafb table make in sm_table().
+ fafb[i][j] : i is the table's step (r)
+ j is the interaction's # (in intype[itype][jtype])
+ dfafb is derivate energy (force)
+ ==================================================================== */
+
+ int itype,jtype,l,m;
+ double r,t1,t2,sds,xi,engBulk,engSurf,fforceBulk,fforceSurf,dcoordloc,dcoupureloc;
+ double engBB,fforceBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2;
+
+ int *type = atom->type;
+ // int n = atom->ntypes;
+
+ itype = map[type[i]];
+ jtype = map[type[j]];
+ m = coultype[itype][jtype];
+
+ r = rsq;
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+
+ iCoord=coord[i];
+ jCoord=coord[j];
+ iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15);
+ jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15);
+
+ // ---- Energies Interpolation
+
+ t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
+ t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
+
+ engBulk = qi*qj*(t1 + (t2 - t1)*xi/2.0);
+ eng=engBulk;
+
+
+ // ---- Forces Interpolation
+
+ t1 = dfafb[l][m] + (dfafb[l+1][m] - dfafb[l][m])*xi;
+ t2 = dfafb[l+1][m] + (dfafb[l+2][m] - dfafb[l+1][m])*(xi-1);
+
+
+ fforce = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
+
+
+ if(strcmp(params[itype].nom,"O")==0 || strcmp(params[jtype].nom,"O")==0){
+
+ if(strcmp(params[itype].nom,"O")==0 && strcmp(params[jtype].nom,"O")==0){
+ // between two oxygens
+
+ t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi;
+ t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0);
+ engSurf = qi*qj*(t1 + (t2 - t1)*xi/2.0);
+
+ t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi;
+ t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0);
+ engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0);
+
+ eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk)) *(engBB-engBulk)
+ + (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf))
+ - (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ;
+
+
+ // ---- Interpolation des forces
+
+ fforceBulk=fforce;
+ t1 = dfafbOxOxSurf[l] + (dfafbOxOxSurf[l+1] - dfafbOxOxSurf[l])*xi;
+ t2 = dfafbOxOxSurf[l+1] + (dfafbOxOxSurf[l+2] - dfafbOxOxSurf[l+1])*(xi-1);
+ fforceSurf = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
+
+ t1 = dfafbOxOxBB[l] + (dfafbOxOxBB[l+1] - dfafbOxOxBB[l])*xi;
+ t2 = dfafbOxOxBB[l+1] + (dfafbOxOxBB[l+2] - dfafbOxOxBB[l+1])*(xi-1);
+ fforceBB = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
+
+ fforce= fforceBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(fforceBB-fforceBulk)
+ + (iIntfCoup2+jIntfCoup2)*((fforceBulk-fforceSurf)/(2*(coordOxBulk-coordOxSurf))
+ - (fforceBB-fforceBulk)/(2*(coordOxBB-coordOxBulk))) ;
+
+ }
+ else{ // between metal and oxygen
+
+ t1 = fafbTiOxSurf[l] + (fafbTiOxSurf[l+1] - fafbTiOxSurf[l])*xi;
+ t2 = fafbTiOxSurf[l+1] + (fafbTiOxSurf[l+2] - fafbTiOxSurf[l+1])*(xi-1.0);
+ engSurf = qi*qj*(t1 + (t2 - t1)*xi/2.0);
+ t1 = fafbTiOxBB[l] + (fafbTiOxBB[l+1] - fafbTiOxBB[l])*xi;
+ t2 = fafbTiOxBB[l+1] + (fafbTiOxBB[l+2] - fafbTiOxBB[l+1])*(xi-1.0);
+ engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0);
+
+ if(strcmp(params[jtype].nom,"O")==0) //the atom j is an oxygen
+ { iIntfCoup2=jIntfCoup2;
+ iCoord=jCoord; }
+
+ eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf) * iIntfCoup2
+ + (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2);
+
+
+ // ---- Forces Interpolation
+
+ fforceBulk=fforce;
+ t1 = dfafbTiOxSurf[l] + (dfafbTiOxSurf[l+1] - dfafbTiOxSurf[l])*xi;
+ t2 = dfafbTiOxSurf[l+1] + (dfafbTiOxSurf[l+2] - dfafbTiOxSurf[l+1])*(xi-1);
+ fforceSurf = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
+
+ t1 = dfafbTiOxBB[l] + (dfafbTiOxBB[l+1] - dfafbTiOxBB[l])*xi;
+ t2 = dfafbTiOxBB[l+1] + (dfafbTiOxBB[l+2] - dfafbTiOxBB[l+1])*(xi-1);
+ fforceBB = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
+
+ dcoordloc = fcoupured(sqrt(r),r1Coord,r2Coord) ;
+
+
+ dcoupureloc = fcoupured(iCoord,coordOxSurf,coordOxBulk) ;
+ dIntfcoup2loc= fcoup2(iCoord,coordOxBulk,0.15)*dcoupureloc ;
+ fforce = fforceBulk + 1/(coordOxBulk-coordOxSurf) * ((fforceBulk-fforceSurf)* iIntfCoup2
+ - (engBulk-engSurf) *dIntfcoup2loc)
+ + 1/(coordOxBB-coordOxBulk) * ((fforceBB-fforceBulk)*(iCoord-coordOxBulk- iIntfCoup2)
+ - (engBB-engBulk) *(dcoordloc-dIntfcoup2loc));
+
+
+ }
+
+
+
+ }
+
+
+}
+
+/* -------------------------------------------------------------------- */
+
+void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
+{
+
+ /* ===================================================================
+ Coulombian potentiel energy calcul between i and j atoms
+ with fafb table make in sm_table().
+ fafb[i][j] : i is the table's step (r)
+ j is the interaction's # (in intype[itype][jtype])
+ dfafb is derivate energy (force)
+ ==================================================================== */
+
+ int itype,jtype,l,m;
+ double r,t1,t2,sds,xi,engBulk,engSurf,dcoordloc,dcoupureloc;
+ double engBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2;
+
+ int *type = atom->type;
+ // int n = atom->ntypes;
+
+ itype = map[type[i]];
+ jtype = map[type[j]];
+ m = coultype[itype][jtype];
+
+ r = rsq;
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+
+ iCoord=coord[i];
+ jCoord=coord[j];
+ iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15);
+ jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15);
+
+ // ---- Energies Interpolation
+
+ t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
+ t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
+
+
+ eng = (t1 + (t2 - t1)*xi/2.0);
+ engBulk=eng;
+
+
+ if(itype==0 || jtype==0){
+
+ if(itype==0 && jtype==0){ // between two oxygens
+
+ t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi;
+ t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0);
+ engSurf = (t1 + (t2 - t1)*xi/2.0);
+
+ t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi;
+ t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0);
+ engBB = (t1 + (t2 - t1)*xi/2.0);
+
+ eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(engBB-engBulk)
+ + (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf))
+ - (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ;
+
+ } else { // between metal and oxygen
+
+ t1 = fafbTiOxSurf[l] + (fafbTiOxSurf[l+1] - fafbTiOxSurf[l])*xi;
+ t2 = fafbTiOxSurf[l+1] + (fafbTiOxSurf[l+2] - fafbTiOxSurf[l+1])*(xi-1.0);
+ engSurf = (t1 + (t2 - t1)*xi/2.0);
+
+ t1 = fafbTiOxBB[l] + (fafbTiOxBB[l+1] - fafbTiOxBB[l])*xi;
+ t2 = fafbTiOxBB[l+1] + (fafbTiOxBB[l+2] - fafbTiOxBB[l+1])*(xi-1.0);
+ engBB = (t1 + (t2 - t1)*xi/2.0);
+
+ if (jtype==0) { //the atom j is an oxygen
+ iIntfCoup2=jIntfCoup2;
+ iCoord=jCoord;
+ }
+
+ eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf)*iIntfCoup2
+ + (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2);
+
+
+ }
+
+
+
+ }
+
+
+}
+
+/* -------------------------------------------------------------------- */
+
+void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot)
+{
+ int l,m,itype,jtype;
+ double sds,xi,t1,t2,r;
+
+ int *type = atom->type;
+
+
+ if (sqrt(rsq) > cutmax) return ;
+
+ itype = map[type[i]];
+ jtype = map[type[j]];
+ m = coultype[itype][jtype];
+
+ r = rsq ;
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+ // ---- Energies Interpolation
+
+ t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
+ t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
+
+ pot = (t1 + (t2 - t1)*xi/2.0) ;
+
+}
+
+/* --------------------------------------------------------------------
+ Oxygen-Oxygen Interaction
+ -------------------------------------------------------------------- */
+
+void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
+ int eflag, double &eng)
+{
+ double r,tmp_exp,tmp;
+ double A = intparam->abuck ;
+ double rho = intparam->rhobuck ;
+
+ r = sqrt(rsq);
+ tmp = - r/rho ;
+ tmp_exp = exp( tmp );
+
+ eng = A * tmp_exp ;
+
+ fforce = A/rho * tmp_exp / r ; //( - )
+
+}
+
+
+void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce,
+ int eflag, double &eng)
+{
+ double r,tmp_exp,tmp;
+ double aOO = intparam->aOO ;
+ double bOO = intparam->bOO ;
+ double r1OO = intparam->r1OO ;
+ double r2OO = intparam->r2OO ;
+
+ r = sqrt(rsq);
+ tmp_exp= exp( bOO* r);
+ eng = aOO * tmp_exp* fcoupure(r,r1OO,r2OO);
+
+ fforce = - (aOO*bOO * tmp_exp * fcoupure(r,r1OO,r2OO)+ aOO*tmp_exp *fcoupured(r,r1OO,r2OO))/ r ; //( - )
+
+}
+
+
+/* ----------------------------------------------------------------------
+ covalente Interaction
+ ----------------------------------------------------------------------*/
+
+
+void PairSMTBQ::tabsm()
+{
+ int k,m;
+ double s,r,tmpb,tmpr,fcv,fcdv;
+
+ memory->create(tabsmb,kmax,maxintsm+1,"pair:tabsmb");
+ memory->create(tabsmr,kmax,maxintsm+1,"pair:tabsmr");
+ memory->create(dtabsmb,kmax,maxintsm+1,"pair:dtabsmb");
+ memory->create(dtabsmr,kmax,maxintsm+1,"pair:dtabsmr");
+
+
+ for (m = 0; m <= maxintparam; m++) {
+
+ if (intparams[m].intsm == 0) continue;
+
+ double rc1 = intparams[m].dc1;
+ double rc2 = intparams[m].dc2;
+ double A = intparams[m].a;
+ double p = intparams[m].p;
+ double Ksi = intparams[m].ksi;
+ double q = intparams[m].q;
+ double rzero = intparams[m].r0;
+ int sm = intparams[m].intsm;
+
+
+ for (k=0; k < kmax; k++)
+ {
+ s = double(k)*ds ; r = sqrt(s);
+ if (k==0) r=10e-30;
+ tmpb = exp( -2.0*q*(r/rzero - 1.0));
+ tmpr = exp( -p*(r/rzero - 1.0));
+
+ if (r <= rc1)
+ {
+
+ // -- Energy
+ tabsmb[k][sm] = Ksi*Ksi * tmpb ;
+ tabsmr[k][sm] = A * tmpr ;
+
+ // -- Force
+ /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
+ (on a donc une unite force/distance). Le programme multiplie ensuite
+ (dans le PairSMTBQ::compute ) dtabsmb par la projection du vecteur r
+ sur un axe x (ou y ou z) pour determiner la composante de la force selon
+ cette direction. Donc tout est ok au final. */
+
+ dtabsmb[k][sm] = - 2.0 *Ksi*Ksi* q/rzero * tmpb /r;
+ dtabsmr[k][sm] = - A * p/rzero * tmpr/r ;
+
+ } // if
+
+ else if (r > rc1 && r <= rc2)
+ {
+
+ // -- Energie
+ fcv = fcoupure(r,intparams[sm].dc1,intparams[sm].dc2);
+ tabsmb[k][sm] = fcv* Ksi*Ksi * tmpb ;
+ tabsmr[k][sm] = fcv* A * tmpr ;
+
+ // -- Force
+ /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
+ (on a donc une unite force/distance). Le programme multiplie ensuite
+ (dans le PairSMTBQ::compute ) d tabsmb par la projection du vecteur
+ r sur un axe x (ou y ou z) pour determiner la composante de la force
+ selon cette direction. Donc tout est ok au final. */
+
+ fcdv = fcoupured(r,intparams[sm].dc1,intparams[sm].dc2);
+ dtabsmb[k][sm] = (fcv*( - 2.0 *Ksi*Ksi* q/rzero * tmpb )+fcdv* Ksi*Ksi * tmpb )/r ;
+ dtabsmr[k][sm] = (fcv*( - A * p/rzero * tmpr )+fcdv*A * tmpr )/r ;
+
+ }
+
+ else
+ {
+
+ // -- Energie
+ tabsmb[k][sm] = 0.0;
+ tabsmr[k][sm] = 0.0;
+
+ // -- Force
+ dtabsmb[k][sm] = 0.0;
+ dtabsmr[k][sm] = 0.0;
+
+ }
+
+
+
+ } // for kmax
+
+
+ } // for maxintparam
+
+}
+
+
+
+
+
+/* -------------------------------------------------------------- */
+
+void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
+ double &fforce, int eflag, double &eng)
+{
+
+ /* ================================================
+ rsq : square of ij distance
+ fforce : repulsion force
+ eng : repulsion energy
+ eflag : Si oui ou non on calcule l'energie
+ =================================================*/
+
+ int l;
+ double r,sds,xi,t1,t2,dt1,dt2,sweet,iq,jq;
+
+ double rrcs = intparam->dc2;
+ int sm = intparam->intsm;
+
+ // printf ("On rentre dans repulsive\n");
+
+
+ r = rsq;
+ if (sqrt(r) > rrcs) return ;
+
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+ t1 = tabsmr[l][sm] + (tabsmr[l+1][sm] - tabsmr[l][sm])*xi ;
+ t2 = tabsmr[l+1][sm] + (tabsmr[l+2][sm] - tabsmr[l+1][sm])*(xi-1.0) ;
+
+ dt1 = dtabsmr[l][sm] + (dtabsmr[l+1][sm] - dtabsmr[l][sm])*xi ;
+ dt2 = dtabsmr[l+1][sm] + (dtabsmr[l+2][sm] - dtabsmr[l+1][sm])*(xi-1.0) ;
+
+ if (strcmp(intparam->mode,"oxide") == 0)
+ {
+ fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0);
+ eng = (t1 + (t2 - t1)*xi/2.0) ;
+ }
+ else if (strcmp(intparam->mode,"metal") == 0)
+ {
+ sweet = 1.0;
+ fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0) * sweet ;
+ eng = (t1 + (t2 - t1)*xi/2.0) * sweet ;
+ }
+
+}
+
+
+/* --------------------------------------------------------------------------------- */
+
+
+void PairSMTBQ::attractive(Intparam *intparam, double rsq,
+ int eflag, int i, double iq, int j, double jq)
+{
+ int itype,l;
+ double r,t1,t2,xi,sds;
+ double dqcov,sweet,dq,mu;
+
+ double rrcs = intparam->dc2;
+ int *type = atom->type;
+ int sm = intparam->intsm;
+
+ itype = map[type[i]];
+
+ r = rsq;
+ if (sqrt(r) > rrcs) return ;
+
+
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+ t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ;
+ t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ;
+
+
+
+ if (strcmp(intparam->mode,"oxide") == 0) {
+ mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto));
+
+// dq = fabs(params[itype].qform) - fabs(iq);
+// dqcov = dq*(2.0*ncov/params[itype].sto - dq);
+
+ sbcov[i] += (t1 + (t2 - t1)*xi/2.0) *params[itype].sto*mu*mu;
+
+// if (i < 10) printf ("i %d, iq %f sbcov %f \n",i,iq,sbcov[i]);
+
+ if (sqrt(r)<r1Coord) { coord[i] += 1 ; }
+ else if (sqrt(r)<r2Coord){ coord[i] += fcoupure(sqrt(r),r1Coord,r2Coord) ;}
+
+
+ }
+ else if (strcmp(intparam->mode,"metal") == 0) {
+ sweet = 1.0;
+ sbmet[i] += (t1 + (t2 - t1)*xi/2.0) * sweet ;
+ }
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::f_att(Intparam *intparam, int i, int j,double rsq, double &fforce)
+{
+ int itype,jtype,l;
+ int *type = atom->type;
+
+ double r,sds,xi,dt1,dt2,dq,dqcovi,dqcovj;
+ double fcov_ij,fcov_ji,sweet,iq,jq,mu;
+
+ int sm = intparam->intsm;
+ double *q = atom->q;
+
+ itype = map[type[i]];
+ jtype = map[type[j]];
+ iq = q[i] ; jq = q[j];
+
+ r = rsq;
+
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+ dt1 = dtabsmb[l][sm] + (dtabsmb[l+1][sm] - dtabsmb[l][sm])*xi ;
+ dt2 = dtabsmb[l+1][sm] + (dtabsmb[l+2][sm] - dtabsmb[l+1][sm])*(xi-1.0) ;
+
+ dq = fabs(params[itype].qform) - fabs(iq);
+ dqcovi = dq*(2.0*ncov/params[itype].sto - dq);
+
+ dq = fabs(params[jtype].qform) - fabs(jq);
+ dqcovj = dq*(2.0*ncov/params[jtype].sto - dq);
+
+ if (strcmp(intparam->mode,"oxide") == 0) {
+//------------------------------------------
+ mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto));
+ fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovi *params[itype].sto*mu*mu;
+ fcov_ji = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovj *params[jtype].sto*mu*mu;
+
+ fforce = 0.5 * ( fcov_ij/sqrt(sbcov[i]*dqcovi + sbmet[i])
+ + fcov_ji/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ;
+ }
+
+ else if (strcmp(intparam->mode,"metal") == 0) {
+//-----------------------------------------------
+ sweet = 1.0;
+ fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * sweet ;
+
+ fforce = 0.5 * fcov_ij*( 1.0/sqrt(sbcov[i]*dqcovi + sbmet[i])
+ + 1.0/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ;
+ }
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::pot_COV(Param *param, int i, double &qforce)
+{
+ double iq,dq,DQ,sign;
+
+ double *q = atom->q;
+ double qform = param->qform;
+ double sto = param->sto;
+
+ sign = qform / fabs(qform);
+ iq = q[i];
+
+ dq = fabs(qform) - fabs(iq);
+ DQ = dq*(2.0*ncov/sto - dq);
+
+ if (fabs(iq) < 1.0e-7 || fabs(sbcov[i]) < 1.0e-7) {
+ qforce = 0.0; }
+ else {
+ qforce = sign*sbcov[i]/sqrt(sbcov[i]*DQ + sbmet[i])*(ncov/sto - dq) ;
+ }
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSMTBQ::potmet(Intparam *intparam, double rsq,
+ int i, double iq, int j, double jq)
+{
+ int l,itype,jtype;
+ int *type = atom->type;
+ double chi,sds,xi,t1,t2,r,dsweet,dq,dqcovi,dqcovj;
+
+ int sm = intparam->intsm;
+ itype = map[type[i]];
+ jtype = map[type[j]];
+
+ r = rsq;
+ sds = r/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+ t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ;
+ t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ;
+
+ dq = fabs(params[itype].qform) - fabs(iq);
+ dqcovi = dq*(2.0*ncov/params[itype].sto - dq);
+
+ dq = fabs(params[jtype].qform) - fabs(jq);
+ dqcovj = dq*(2.0*ncov/params[jtype].sto - dq);
+
+ dsweet = 0.0;
+ chi = (t1 + (t2 - t1)*xi/2.0) * dsweet *( 1.0/(2.0*sqrt(sbcov[i]*dqcovi+sbmet[i]))
+ + 1.0/(2.0*sqrt(sbcov[j]*dqcovj+sbmet[j])) );
+
+ return chi;
+}
+
+
+/* ----------------------------------------------------------------------
+ Cutting Function
+ ----------------------------------------------------------------------*/
+
+
+/* -------------------------------------------------------------------- */
+
+double PairSMTBQ::fcoupure(double r, double rep_dc1, double rep_dc2)
+{
+ double ddc,a3,a4,a5,x;
+
+ if (r<rep_dc1)
+ {return 1;}
+ else if (r> rep_dc2)
+ {return 0;}
+ else
+ {
+
+ ddc = rep_dc2 - rep_dc1;
+ x = r - rep_dc2;
+
+ a3 = -10/(ddc*ddc*ddc);
+ a4 = -15/(ddc*ddc*ddc*ddc);
+ a5 = -6/(ddc*ddc*ddc*ddc*ddc);
+
+ return x*x*x*(a3 + x*(a4 + x*a5));}
+}
+
+/* ----------------------------------------------------------------------
+ Derivate of cutting function
+ ----------------------------------------------------------------------*/
+
+
+/* ----------------------------------------------------------------------- */
+
+double PairSMTBQ::fcoupured(double r, double rep_dc1, double rep_dc2)
+{
+
+ double ddc,a3,a4,a5,x;
+
+ if ( r>rep_dc1 && r<rep_dc2) {
+ ddc = rep_dc2 - rep_dc1;
+ x = r - rep_dc2;
+
+ a3 = -10/(ddc*ddc*ddc);
+ a4 = -15/(ddc*ddc*ddc*ddc);
+ a5 = -6/(ddc*ddc*ddc*ddc*ddc);
+
+ return x*x*(3*a3 + x*(4*a4 + 5*x*a5));}
+ else {return 0;}
+}
+
+
+/* ----------------------------------------------------------------------
+ cutting function for derive (force)
+ ----------------------------------------------------------------------*/
+
+
+/* -------------------------------------------------------------------- */
+
+
+
+double PairSMTBQ::fcoup2(double c, double x, double delta)
+{
+ double dc;
+
+ if (c<x-delta)
+ {return 1;}
+ else if (c> x+delta)
+ {return 0;}
+ else
+ {
+ dc = c - x-delta;
+ return dc*dc*(3*delta+dc)/(4*delta*delta*delta);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Primitive of cutting function for derive (force)
+ ----------------------------------------------------------------------*/
+
+
+/* -------------------------------------------------------------------- */
+
+double PairSMTBQ::Primfcoup2(double c, double x, double delta)
+{
+
+ return (c*(c*c*c - 4* c*c* x - 4* (x - 2 *delta) * (x+delta)*(x+delta) +
+ 6* c *(x*x - delta*delta)))/(16* delta*delta*delta);
+
+}
+
+
+/* ----------------------------------------------------------------------
+ Integral of cutting function for derive (force) between x and c
+ ----------------------------------------------------------------------*/
+
+
+/* -------------------------------------------------------------------- */
+
+double PairSMTBQ::Intfcoup2(double c, double x, double delta)
+{
+
+ if (c<x-delta)
+ {return c - x + delta + Primfcoup2(x-delta,x,delta) - Primfcoup2(x,x,delta) ;}
+ else if (c> x+delta)
+ {return Primfcoup2(x+delta,x,delta) - Primfcoup2(x,x,delta) ;}
+ else
+ {
+ return Primfcoup2(c,x,delta) - Primfcoup2(x,x,delta) ;}
+}
+
+
+/* ---------------------------------------------------------------------
+ Energy derivation respect charge Q
+ --------------------------------------------------------------------- */
+
+void PairSMTBQ::QForce_charge(int loop)
+{
+ int i,j,ii,jj,jnum;
+ int itype,jtype,m,gp;
+ double xtmp,ytmp,ztmp,evdwlCoul,fpairCoul;
+ double rsq,delr[3],chi_ij;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double iq,jq,fqi,fqj,fqij,fqij2,fqjj;
+ int eflag;
+
+
+ double **x = atom->x;
+ double *q = atom->q;
+ int *type = atom->type;
+ int step = update->ntimestep;
+
+ int inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ int nlocal = atom->nlocal;
+
+
+ // loop over full neighbor list of my atoms
+
+ fqi = fqj = fqij = fqij2 = fqjj = 0.0;
+
+
+ // ==================
+ if (loop == 0) {
+ // ==================
+
+
+
+ for (ii = 0; ii < inum; ii ++) {
+ //--------------------------------
+ i = ilist[ii];
+ itype = map[type[i]];
+
+ gp = flag_QEq[i];
+
+ sbcov[i] =coord[i]= sbmet[i] = 0.0;
+
+ itype = map[type[i]];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ iq = q[i];
+
+
+
+
+ // two-body interactions
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+// -------------------------------
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ jtype = map[type[j]];
+ jq = q[j];
+
+ m = intype[itype][jtype];
+ if (intparams[m].intsm == 0) continue ;
+
+
+ delr[0] = x[j][0] - xtmp;
+ delr[1] = x[j][1] - ytmp;
+ delr[2] = x[j][2] - ztmp;
+ rsq = vec3_dot(delr,delr);
+
+
+// Covalente charge forces - sbcov initialization
+// ------------------------------------------------
+ if (sqrt(rsq) > intparams[m].dc2) continue;
+
+ attractive (&intparams[m],rsq,eflag,i,iq,j,jq);
+
+
+ } // ---------------------------------------------- for jj
+
+
+ } // -------------------------------------------- ii
+
+ // ===============================================
+ // Communicates the tables *sbcov and *sbmet
+ // to calculate the N-body forces
+ // ================================================
+
+ forward (sbcov) ; reverse (sbcov);
+ forward (coord) ; reverse (coord);
+ forward (sbmet) ; reverse (sbmet);
+
+
+ if (nteam == 0) return; //no oxide
+ if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0) return;
+
+ // =======================
+ } // End of If(loop)
+ // =======================
+
+
+ // ===============================================
+
+ for (ii=0; ii<inum; ii++)
+ {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i]; iq = q[i];
+
+ potmad[i] = potself[i] = potcov[i] = 0.0 ;
+
+ if (gp == 0) continue;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ fqi = 0.0 ;
+
+ // Madelung potential
+ // --------------------
+ potmad[i] += 2.0*Vself*iq ;
+
+ // charge force from self energy
+ // -----------------------------
+ fqi = qfo_self(¶ms[itype],iq);
+ potself[i] = fqi ;
+
+
+
+ // Loop on Second moment neighbor
+ // -------------------------------
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++)
+ {
+ j = jlist[jj];
+ jtype = map[type[j]];
+ m = intype[itype][jtype];
+ jq = q[j];
+
+
+ delr[0] = x[j][0] - xtmp;
+ delr[1] = x[j][1] - ytmp;
+ delr[2] = x[j][2] - ztmp;
+ rsq = vec3_dot(delr,delr);
+
+ // long range q-dependent
+ if (sqrt(rsq) > cutmax) continue;
+
+ // 1/r charge forces
+ // --------------------
+ fqij = 0.0;
+// pot_ES2 (i,j,rsq,fqij2);
+ pot_ES (i,j,rsq,fqij);
+
+ potmad[i] += jq*fqij ;
+
+
+ } // ------ jj
+
+ fqi = 0.0;
+ pot_COV (¶ms[itype],i,fqi) ;
+ potcov[i] = fqi ;
+
+
+ } // ------- ii
+
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::Charge()
+{
+ int i,ii,iloop,itype,gp,m;
+ int *ilist;
+ double heatpq,qmass,dtq,dtq2,qtot,qtotll;
+ double t_init,t_end,dt;
+
+ double *Transf,*TransfAll;
+
+ double *q = atom->q;
+ double **x = atom->x;
+ int *type = atom->type;
+ int step = update->ntimestep;
+
+ int inum = list->inum;
+ ilist = list->ilist;
+
+
+ if (me == 0) t_init = MPI_Wtime();
+ if (step == 0) cluster = 0;
+
+ // ---------------------------
+ // Mise en place des groupes
+ // ---------------------------
+
+ if (strcmp(QEqMode,"BulkFromSlab") == 0)
+ groupBulkFromSlab_QEq();
+ else if (strcmp(QEqMode,"QEqAll") == 0)
+ groupQEqAll_QEq();
+ else if (strcmp(QEqMode,"QEqAllParallel") == 0)
+ groupQEqAllParallel_QEq();
+ else if (strcmp(QEqMode,"Surface") == 0)
+ groupSurface_QEq();
+
+
+
+ if (nteam+1 != cluster) {
+ memory->destroy(nQEqall);
+ memory->destroy(nQEqaall);
+ memory->destroy(nQEqcall);
+
+ cluster = nteam+1;
+ memory->create(nQEqall,nteam+1,"pair:nQEq");
+ memory->create(nQEqaall,nteam+1,"pair:nQEqa");
+ memory->create(nQEqcall,nteam+1,"pair:nQEqc");
+ }
+ // ---------------------------
+
+
+ double enegtotall[nteam+1],enegchkall[nteam+1],enegmaxall[nteam+1],qtota[nteam+1],qtotc[nteam+1];
+ double qtotcll[nteam+1],qtotall[nteam+1];
+ double sigmaa[nteam+1],sigmac[nteam+1],sigmaall[nteam+1],sigmacll[nteam+1];
+ int end[nteam+1], nQEq[nteam+1],nQEqc[nteam+1],nQEqa[nteam+1];
+
+
+ iloop = 0;
+
+
+ heatpq = 0.07;
+ qmass = 0.000548580;
+ dtq = 0.0006; // 0.0006
+ dtq2 = 0.5*dtq*dtq/qmass;
+
+ double enegchk[nteam+1];
+ double enegtot[nteam+1];
+ double enegmax[nteam+1];
+
+
+
+ for (i=0; i<nteam+1; i++) {
+ nQEq[i] = nQEqa[i] = nQEqc[i] = 0;
+ nQEqall[i] = nQEqcall[i] = nQEqaall[i] = end[i]= 0;
+ enegchk[i] = enegtot[i] = enegmax[i] = 0.0;
+ qtota[i] = qtotc[i] = qtotall[i] = qtotcll[i] = 0.0;
+ sigmaall[i] = sigmacll[i] = 0.0;
+ }
+ qtot = qtotll = 0.0 ;
+
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i];
+ q1[i] = q2[i] = qf[i] = 0.0;
+
+ qtot += q[i] ;
+ nQEq[gp] += 1;
+ if (itype != 0) { qtotc[gp] += q[i]; nQEqc[gp] += 1; }
+ if (itype == 0) { qtota[gp] += q[i]; nQEqa[gp] += 1; }
+ }
+
+ MPI_Allreduce(nQEq,nQEqall,nteam+1,MPI_INT,MPI_SUM,world);
+ MPI_Allreduce(nQEqc,nQEqcall,nteam+1,MPI_INT,MPI_SUM,world);
+ MPI_Allreduce(nQEqa,nQEqaall,nteam+1,MPI_INT,MPI_SUM,world);
+
+ MPI_Allreduce(qtotc,qtotcll,nteam+1,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(qtota,qtotall,nteam+1,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(&qtot,&qtotll,1,MPI_DOUBLE,MPI_SUM,world);
+
+
+ // ---------------------------------
+ // Init_charge(nQEq,nQEqa,nQEqc);
+ // ---------------------------------
+
+ if (update->ntimestep == 0 && (strcmp(QInitMode,"true") == 0) ) {
+ //Carefull here it won't be fine if there are more than 2 species!!!
+ QOxInit=max(QOxInit, -0.98* params[1].qform *nQEqcall[gp]/nQEqaall[gp]) ;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i];
+
+// if (gp == 0) continue;
+
+ if (itype == 0) q[i] = QOxInit ;
+ if (itype > 0) q[i] = -QOxInit * nQEqaall[gp]/nQEqcall[gp];
+ }
+ }
+
+ if (nteam == 0 || Qstep == 0) return;
+ if (fmod(double(step), double(Qstep)) != 0.0) return;
+ // --------------------------------------
+
+ // ----
+
+ // ----
+
+
+ if (me == 0 && strcmp(Bavard,"false") != 0) {
+ for (gp = 0; gp < nteam+1; gp++) {
+ printf (" ++++ Groupe %d - Nox %d Ncat %d\n",gp,nQEqaall[gp],nQEqcall[gp]);
+ if (nQEqcall[gp] !=0 && nQEqaall[gp] !=0 )
+ printf (" neutralite des charges %f\n qtotc %f qtota %f\n",
+ qtotll,qtotcll[gp]/nQEqcall[gp],qtotall[gp]/nQEqaall[gp]);
+ printf (" ---------------------------- \n");}
+ }
+
+ // ======================= Tab transfert ==================
+ // Transf[gp] = enegtot[gp]
+ // Transf[gp+cluster] = Qtotc[gp]
+ // Transf[gp+2cluster] = Qtota[gp]
+ // Transf[3cluster] = Qtot
+ // -------------------------------------------------------
+ memory->create(Transf,3*cluster+1,"pair:Tranf");
+ memory->create(TransfAll,3*cluster+1,"pair:TranfAll");
+ // ========================================================
+
+
+ // --------------------------------------------
+ for (iloop = 0; iloop < loopmax; iloop ++ ) {
+ // --------------------------------------------
+
+ qtot = qtotll = Transf[3*cluster] = 0.0 ;
+ for (gp=0; gp<nteam+1; gp++) {
+ Transf[gp] = Transf[gp+cluster] = Transf[gp+2*cluster] = 0.0;
+ TransfAll[gp] = TransfAll[gp+cluster] = TransfAll[gp+2*cluster] = 0.0;
+ enegtot[gp] = enegtotall[gp] = enegchkall[gp] = enegmaxall[gp] = 0.0 ;
+ }
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ q[i] += q1[i];
+
+ Transf[3*cluster] += q[i];
+ itype = map[type[i]];
+ gp = flag_QEq[i];
+ if (itype == 0) Transf[gp+2*cluster] += q[i];
+ if (itype != 0) Transf[gp+cluster] += q[i];
+ }
+
+ // Communication des charges
+ // ---------------------------
+ forward(q) ; reverse(q);
+
+
+ // Calcul des potentiel
+ // ----------------------
+ QForce_charge(iloop);
+
+// exit(1);
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i];
+
+ qf[i] = 0.0;
+ qf[i] = potself[i]+potmad[i]+potcov[i]+chimet[i] ;
+ Transf[gp] += qf[i];
+ }
+
+ MPI_Allreduce(Transf,TransfAll,3*cluster+1,MPI_DOUBLE,MPI_SUM,world);
+
+ for (i = 0; i < nteam+1; i++) {
+
+ if (nQEqall[i] !=0) TransfAll[i] /= double(nQEqall[i]);
+ enegchk[i] = enegmax[i] = 0.0;
+ }
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = map[type[i]];
+ gp = flag_QEq[i];
+
+ if (gp == 0) continue;
+
+ q2[i] = TransfAll[gp] - qf[i];
+
+ enegmax[gp] = MAX(enegmax[gp],fabs(q2[i]));
+ enegchk[gp] += fabs(q2[i]);
+ qf[i] = q2[i];
+
+ } // Boucle local
+
+ MPI_Allreduce(enegchk,enegchkall,nteam+1,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(enegmax,enegmaxall,nteam+1,MPI_DOUBLE,MPI_MAX,world);
+
+
+ for (gp = 0; gp < nteam+1; gp++) {
+ if(nQEqall[gp] !=0) {
+ enegchk[gp] = enegchkall[gp]/double(nQEqall[gp]);
+ enegmax[gp] = enegmaxall[gp];
+ }
+ }
+
+ // -----------------------------------------------------
+ // Convergence Test
+ // -----------------------------------------------------
+
+ m = 0;
+ for (gp = 1; gp < nteam+1; gp++) {
+ if (enegchk[gp] <= precision && enegmax[gp] <= 100.0*precision) end[gp] = 1;
+ }
+ for (gp = 1; gp < nteam+1; gp++) { m += end[gp] ; }
+
+ if (m == nteam) { break; }
+ // -----------------------------------------------------
+ // -----------------------------------------------------
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ }
+
+ // --------------------------------------------
+ } // -------------------------------- iloop
+ // --------------------------------------------
+
+
+ // =======================================
+ // Charge Communication.
+ // =======================================
+ forward(q); reverse(q);
+
+ //:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+ // ==========================================
+ // Ecriture des potentiels dans un fichier
+ // ==========================================
+
+ if (strcmp(writepot,"true") == 0 && fmod(double(step), Neverypot) == 0.0) {
+
+ ofstream fichierpot("Electroneg_component.txt", ios::out | ios::trunc) ;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = map[type[i]];
+ gp = flag_QEq[i];
+
+
+ if (fichierpot) fichierpot<< setprecision(9) <<i <<" "<<itype<<" "<<x[i][0]<<" "<<x[i][1]
+ <<" "<<x[i][2]<<" "<<q[i]<<" "<<potself[i] + potmad[i]<<" "<<potcov[i]
+ <<" "<<sbcov[i]<<" "<<TransfAll[gp]<<endl;
+
+ }
+ if (fichierpot) fichierpot.close() ;
+ }
+
+ //:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+ // Statistique (ecart type)
+ // ------------------------
+ for (i=0; i<nteam+1; i++) {
+ if(nQEqcall[i] !=0)
+ { TransfAll[i+cluster] /= double(nQEqcall[i]) ;
+ TransfAll[i+2*cluster] /= double(nQEqaall[i]) ;}
+ sigmaa[i] = sigmac[i] = 0.0;
+ }
+
+ qtot = 0.0 ;
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii];
+ itype = map[type[i]];
+ gp = flag_QEq[i];
+ // qtot += q[i];
+
+ if (gp == 0) continue;
+
+ if (itype == 0) sigmaa[gp] += (q[i]-TransfAll[gp+2*cluster])*(q[i]-TransfAll[gp+2*cluster]);
+ if (itype == 1) sigmac[gp] += (q[i]-TransfAll[gp+cluster])*(q[i]-TransfAll[gp+cluster]);
+ }
+
+ MPI_Allreduce(sigmaa,sigmaall,nteam+1,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(sigmac,sigmacll,nteam+1,MPI_DOUBLE,MPI_SUM,world);
+
+ for (gp = 1; gp < nteam+1; gp++) {
+ sigmaall[gp] = sqrt(sigmaall[gp]/double(nQEqaall[gp])) ;
+ sigmacll[gp] = sqrt(sigmacll[gp]/double(nQEqcall[gp])) ;
+ }
+
+
+
+ if (me == 0 && strcmp(Bavard,"false") != 0){
+ for (gp = 0; gp < nteam+1; gp++) {
+ printf (" -------------- Groupe %d -----------------\n",gp);
+ printf (" qtotc %f(+- %f) qtota %f(+- %f)\n",
+ TransfAll[gp+cluster],sigmacll[gp],TransfAll[gp+2*cluster],sigmaall[gp]);
+ printf (" Potentiel elec total : %f\n iloop %d, qtot %f\n",TransfAll[gp],iloop,TransfAll[3*cluster]);
+ printf (" convergence : %f - %f\n",enegchk[gp],enegmax[gp]);
+ }
+
+ t_end = MPI_Wtime();
+ dt = t_end - t_init;
+ printf (" temps dans charges : %f seconde. \n",dt);
+ printf (" ======================================================== \n");
+ }
+
+ // ============== Destroy Tab
+ memory->destroy(Transf);
+ memory->destroy(TransfAll);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::groupBulkFromSlab_QEq()
+{ int ii,i;
+ double **x=atom->x;
+ int *ilist;
+ double ztmp;
+ int inum = list->inum;
+ ilist = list->ilist;
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii];
+ ztmp = x[i][2];
+ if (ztmp>zlim1QEq && ztmp< zlim2QEq)
+ flag_QEq[i]=1;
+ else
+ flag_QEq[i]=0;
+
+ nteam=1;
+
+ }
+
+}
+
+// ----------------------------------------------
+
+void PairSMTBQ::groupQEqAll_QEq()
+{ int ii,i;
+ int *ilist;
+ int inum = list->inum;
+ ilist = list->ilist;
+
+ nteam=1;
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i= ilist[ii];
+ flag_QEq[i]=1;
+ }
+
+}
+
+// ----------------------------------------------
+
+void PairSMTBQ::groupSurface_QEq()
+{ int ii,i;
+ double **x=atom->x;
+ int *ilist;
+ double ztmp;
+ int inum = list->inum;
+ ilist = list->ilist;
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii];
+ ztmp = x[i][2];
+ if (ztmp>zlim1QEq)
+ flag_QEq[i]=1;
+ else
+ flag_QEq[i]=0;
+
+ nteam=1;
+
+ }
+
+}
+
+
+void PairSMTBQ::groupQEqAllParallel_QEq()
+{
+ int ii,i,jj,j,kk,k,itype,jtype,ktype,jnum,m,gp,zz,z,kgp;
+ int iproc,team_elt[10][nproc],team_QEq[10][nproc][5];
+ int *ilist,*jlist,*numneigh,**firstneigh,ngp,igp,nboite;
+ double delr[3],xtmp,ytmp,ztmp,rsq;
+ int **flag_gp, *nelt, **tab_gp;
+ int QEq,QEqall[nproc];
+
+ double **x = atom->x;
+ int *type = atom->type;
+ int inum = list->inum;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+
+ // +++++++++++++++++++++++++++++++++++++++++++++++++
+ // On declare et initialise nos p'tits tableaux
+ // +++++++++++++++++++++++++++++++++++++++++++++++++
+
+ nboite = nlocal + nghost;
+ int **tabtemp,**Alltabtemp, *gptmp, *Allgptmp;
+
+ memory->create(tabtemp,10*nproc+10,nproc,"pair:tabtemp");
+ memory->create(Alltabtemp,10*nproc+10,nproc,"pair:Alltabtemp");
+ memory->create(gptmp,10*nproc+10,"pair:gptmp");
+ memory->create(Allgptmp,10*nproc+10,"pair:Allgptmp");
+
+ memory->create(flag_gp,nproc,nboite,"pair:flag_gp");
+ memory->create(nelt,nboite,"pair:nelt");
+ memory->create(tab_gp,10,nboite,"pair:flag_gp");
+
+
+ for (i = 0; i < nlocal+nghost ; i++) { flag_QEq[i] = 0; }
+ for (i = 0; i < 10*nproc; i++) {
+ gptmp[i] = 0; Allgptmp[i] = 0;
+ for (j=0;j<nproc;j++) { tabtemp[i][j] = 0;
+ Alltabtemp[i][j] = 0;}
+ }
+ for (i = 0; i < 10; i++) {
+ for (k = 0; k < nboite; k++) { tab_gp[i][k] = 0;
+ if (i == 0) nelt[k] = 0;
+ }
+ for (j = 0; j < nproc; j++) {
+ team_elt[i][j] = 0;
+ for (k = 0; k < 5; k++) { team_QEq[i][j][k] = 0; }
+ }
+ }
+
+ QEq = 0;
+
+
+ // printf ("groupeQEq me %d - nloc %d nghost %d boite %d\n",
+ // me,nlocal,nghost,nboite);
+
+ // ++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ // On identifie les atomes rentrant dans le schema QEq +
+ // ++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii] ; itype = map[type[i]] ;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ for (jj = 0; jj < jnum; jj++ )
+ {
+ j = jlist[jj] ; jtype = map[type[j]];
+ if (jtype == itype) continue;
+ m = intype[itype][jtype];
+
+ delr[0] = x[j][0] - xtmp;
+ delr[1] = x[j][1] - ytmp;
+ delr[2] = x[j][2] - ztmp;
+ rsq = vec3_dot(delr,delr);
+
+ if (sqrt(rsq) <= intparams[m].dc2) {
+ flag_QEq[i] = 1; flag_QEq[j] = 1;
+ }
+ }
+ if (flag_QEq[i] == 1) {
+ QEq = 1;
+ }
+ }
+
+ // ::::::::::::::: Testing the presence of oxide :::::::::::
+ m = 0;
+ MPI_Allgather(&QEq,1,MPI_INT,QEqall,1,MPI_INT,world);
+ for (iproc = 0; iproc < nproc; iproc++) {
+ if (QEqall[iproc] == 1) m = 1;
+ }
+ if (m == 0) {
+ memory->destroy(tabtemp);
+ memory->destroy(Alltabtemp);
+ memory->destroy(gptmp);
+ memory->destroy(Allgptmp);
+ memory->destroy(flag_gp);
+ memory->destroy(tab_gp);
+ memory->destroy(nelt);
+
+ return;
+ }
+ // :::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+ for (m = 0; m < nproc; m++) {
+ for (i = 0; i < nboite; i++) { flag_gp[m][i] = 0; }
+ }
+
+ // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
+ // It includes oxygens entering the QEq scheme O
+ // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
+
+
+ ngp = igp = 0; nelt[ngp] = 0;
+
+ // On prend un oxyg�ne
+ // printf ("[me %d] On prend un oxygene\n",me);
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii] ; itype = map[type[i]];
+ if (itype != 0 || flag_QEq[i] == 0) continue;
+
+ m = 0;
+
+ if (ngp != 0 && flag_gp[me][i] == ngp) continue;
+
+
+ // Grouping Initialisation
+ // -----------------------------
+ if (flag_gp[me][i] == 0) {
+ ngp += 1; nelt[ngp] = 0;
+ tab_gp[ngp][nelt[ngp]] = i;
+ flag_gp[me][i] = ngp;
+ nelt[ngp] += 1;
+ }
+ // -------------------------------
+
+
+ // Loop on the groups
+ // ----------------------
+ for (kk = 0; kk < nelt[ngp]; kk++)
+ {
+ k = tab_gp[ngp][kk];
+ ktype = map[type[k]];
+ // printf ("[me %d] kk - gp %d elemt %d : atom %d(%d)\n",me,ngp,kk,k,ktype);
+ if (k >= nlocal) continue;
+
+ xtmp = x[k][0];
+ ytmp = x[k][1];
+ ztmp = x[k][2];
+
+ // Loop on the oxygen's neighbor of the group
+ // ---------------------------------------------
+ jlist = firstneigh[k];
+ jnum = numneigh[k];
+ for (j = 0; j < nboite; j++ )
+ {
+ jtype = map[type[j]];
+ if (jtype == ktype) continue;
+ m = intype[itype][jtype];
+
+ if (jtype == 0 && flag_QEq[j] == 0) continue;
+
+
+ if (flag_gp[me][j] == ngp) continue;
+
+ delr[0] = x[j][0] - xtmp;
+ delr[1] = x[j][1] - ytmp;
+ delr[2] = x[j][2] - ztmp;
+ rsq = vec3_dot(delr,delr);
+
+ // -------------------------------------
+ if (sqrt(rsq) <= cutmax) {
+
+ flag_QEq[j] = 1; //Entre dans le schema QEq
+
+ // :::::::::::::::::::: Meeting of two group in the same proc :::::::::::::::::::::
+
+ if (flag_gp[me][j] != 0 && flag_gp[me][j] != ngp && nelt[flag_gp[me][j]] != 0) {
+ printf("[me %d] (atom %d) %d [elt %d] rencontre un nouveau groupe %d [elt %d] (atom %d)\n",
+ me,k,ngp,nelt[ngp],flag_gp[me][j],nelt[flag_gp[me][j]],j);
+
+ // On met a jours les tableaux
+ // -----------------------------
+ igp = flag_gp[me][j];
+ z = min(igp,ngp);
+
+ if (z == igp) { igp = z; }
+ else if (z == ngp) {
+ ngp = igp ; igp = z;
+ flag_gp[me][j] = ngp;
+ }
+
+ for (zz = 0; zz < nelt[ngp]; zz++) {
+ z = tab_gp[ngp][zz];
+ tab_gp[igp][nelt[igp]] = z;
+ nelt[igp] += 1;
+ flag_gp[me][z] = igp;
+ tab_gp[ngp][zz] = 0;
+ }
+
+ nelt[ngp] = 0;
+ for (z = nlocal; z < nboite; z++) {
+ if (flag_gp[me][z] == ngp) flag_gp[me][z] = igp;
+ }
+
+ m = 1; kk = 0;
+ ngp = igp;
+ break;
+ }
+ // ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+ flag_gp[me][j] = ngp;
+ if (j < nlocal)
+ {
+ tab_gp[ngp][nelt[ngp]] = j;
+ nelt[ngp] += 1;
+ }
+ }
+ } // for j
+ } // for k
+ } // for ii
+
+ // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
+ // Groups communication
+ // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
+ for (i = 0; i < nproc; i++) {
+ forward_int(flag_gp[i]); reverse_int(flag_gp[i]);
+ }
+ // ---
+
+
+ // =======================================================
+ // Loop on the cation to make them joined in the oxygen's
+ // group which it interacts
+ // =======================================================
+ igp = 0;
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii] ; itype = map[type[i]];
+ if (itype == 0) continue;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ for (jj = 0; jj < jnum; jj++ )
+ {
+ j = jlist[jj] ; jtype = map[type[j]];
+ if (jtype != 0) continue;
+
+ m = 0;
+ for (iproc = 0; iproc < nproc; iproc++) {
+ if (flag_gp[iproc][j] != 0) m = flag_gp[iproc][j];
+ }
+ if (m == 0) continue;
+
+ delr[0] = x[j][0] - xtmp;
+ delr[1] = x[j][1] - ytmp;
+ delr[2] = x[j][2] - ztmp;
+ rsq = vec3_dot(delr,delr);
+
+ // ----------------------------------------
+ if (sqrt(rsq) <= cutmax) {
+ // if (sqrt(rsq) <= intparams[m].dc2) {
+ // ----------------------------------------
+
+ flag_QEq[i] = 1; igp = flag_gp[me][j];
+
+ if (flag_gp[me][i] == 0) flag_gp[me][i] = igp;
+
+ if (flag_gp[me][i] != igp && igp != 0) {
+ printf ("[me %d] Cation i %d gp %d [nelt %d] rencontre j %d(%d)du groupe %d [nelt %d]\n",
+ me,i,flag_gp[me][i],nelt[flag_gp[me][i]],j,jtype,igp,nelt[igp]);
+
+ igp = min(flag_gp[me][i],flag_gp[me][j]);
+ if (igp == flag_gp[me][i]) { kgp = flag_gp[me][j]; }
+ else { kgp = flag_gp[me][i]; }
+
+ for (k = 0; k < nelt[kgp]; k++) {
+ z = tab_gp[kgp][k];
+ tab_gp[igp][nelt[igp]] = z;
+ nelt[igp] += 1;
+ flag_gp[me][z] = igp;
+ tab_gp[kgp][k] = 0;
+ }
+ nelt[kgp] = 0;
+
+ for (k = 0; k < nboite; k++) {
+ if (flag_gp[me][k] == kgp) flag_gp[me][k] = igp;
+ }
+
+ }
+ m = 0;
+ for (k = 0; k < nelt[igp]; k++) {
+ if (tab_gp[igp][k] == i) m = 1;
+ }
+
+ if (i >= nlocal || m == 1 ) continue;
+ // printf ("[me %d] igp %d - nelt %d atom %d\n",me,igp,nelt[igp],i);
+ tab_gp[igp][nelt[igp]] = i;
+ nelt[igp] += 1;
+ break;
+ }
+
+ } // voisin j
+
+ } // atom i
+
+ /* ==================================================
+ Group Communication between proc for unification
+ ================================================== */
+ for (i = 0; i < nproc; i++) {
+ forward_int(flag_gp[i]); reverse_int(flag_gp[i]);
+ }
+
+ // =============== End of COMM =================
+
+
+ for (i = 0; i < nboite; i++) {
+
+ m = 10*me + flag_gp[me][i];
+ if (m == 10*me) continue; // Pas de groupe zero
+ gptmp[m] = 1;
+ for (k = 0; k < nproc; k++) {
+
+ if (k == me) continue;
+ if (tabtemp[m][k] != 0) continue;
+
+ if (flag_gp[k][i] != 0) {
+ tabtemp[m][k] = 10*k + flag_gp[k][i];
+ }
+ }
+
+ }
+
+ for (k = 0; k < 10*nproc; k++) {
+ MPI_Allreduce(tabtemp[k],Alltabtemp[k],nproc,MPI_INT,MPI_SUM,world); }
+ MPI_Allreduce(gptmp,Allgptmp,10*nproc,MPI_INT,MPI_SUM,world);
+
+ nteam = 0; iproc = 0;
+ for (igp = 0; igp < 10*nproc; igp++) {
+ if (Allgptmp[igp] == 0) continue;
+ iproc = int(double(igp)/10.0);
+ ngp = igp - 10*iproc;
+ if (nteam == 0) {
+
+ nteam += 1;
+ team_elt[nteam][iproc] = 0;
+ team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp;
+ team_elt[nteam][iproc] += 1;
+ } else {
+ m = 0;
+ for (i = 1; i < nteam+1; i++) {
+ for (k = 0; k < team_elt[i][iproc]; k++) {
+ if (ngp == team_QEq[i][iproc][k]) m = 1;
+ } }
+ if (m == 1) continue;
+ // create a new team!!
+ // ---------------------------
+ if (m == 0) {
+ nteam += 1;
+ team_elt[nteam][iproc] = 0;
+ team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp;
+ team_elt[nteam][iproc] += 1;
+ }
+ }
+ // -------
+ // On a mis une graine dans le groupe et nous allons
+ // remplir se groupe en questionnant le "tabtemp[igp][iproc]=jgp"
+ //
+ for (kk = 0; kk < nproc; kk++) {
+ for (k = 0; k < team_elt[nteam][kk]; k++) {
+
+ // On prend le gp le k ieme element de la team nteam sur le proc iproc
+ // ngp = 0;
+ ngp = team_QEq[nteam][kk][k];
+ kgp = 10*kk + ngp;
+
+ // On regarde sur les autre proc si ce gp ne pointe pas vers un autre.
+ for (i = 0; i < nproc; i++) {
+ if (i == kk) continue;
+ if (Alltabtemp[kgp][i] == 0) continue;
+
+ if (Alltabtemp[kgp][i] != 0) ngp = Alltabtemp[kgp][i];
+ ngp = ngp - 10*i;
+
+ // Est ce que ce groupe est nouveau?
+ m = 0;
+ for (j = 0; j < team_elt[nteam][i]; j++) {
+ if (team_QEq[nteam][i][j] == ngp) m = 1;
+ }
+
+ if (m == 0) {
+ iproc = i; k = 0;
+ team_QEq[nteam][i][team_elt[nteam][i]] = ngp ;
+ team_elt[nteam][i] += 1;
+ }
+ } // regard sur les autre proc
+
+ } // On rempli de proche en proche
+ } // boucle kk sur les proc
+ }
+
+ // Finalement on met le numero de la team en indice du flag_QEq, c mieu!
+ // ---------------------------------------------------------------------
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii]; m = 0; itype = map[type[i]];
+ if (flag_QEq[i] == 0) continue;
+
+ gp = flag_gp[me][i];
+ for (j = 1; j <= nteam; j++) {
+ for (k = 0; k < team_elt[j][me]; k++) {
+ if (gp == team_QEq[j][me][k]) {
+ flag_QEq[i] = j; m = 1;
+ break;
+ }
+ }
+ if (m == 1) break;
+ }
+ }
+
+ memory->destroy(tabtemp);
+ memory->destroy(Alltabtemp);
+ memory->destroy(gptmp);
+ memory->destroy(Allgptmp);
+ memory->destroy(flag_gp);
+ memory->destroy(tab_gp);
+ memory->destroy(nelt);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
+{
+ int ii,i,gp,itype;
+ int *ilist,test[nteam],init[nteam];
+ double bound,tot,totll;
+
+ int inum = list->inum;
+ int *type = atom->type;
+ double *q = atom->q;
+ ilist = list->ilist;
+
+ if (nteam == 0) return;
+
+ if (me == 0) printf (" ======== Init_charge ======== \n");
+ for (gp = 0; gp < cluster; gp++) {
+ test[gp] = 0; init[gp] = 0;
+ }
+
+
+ // On fait un test sur les charges pour voir sont
+ // elles sont dans le domaine delimiter par DeltaQ
+ // -------------------------------------------------
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i];
+
+ if (gp != 0 && itype == 0) {
+ bound = fabs(2.0*ncov/params[itype].sto - fabs(params[itype].qform)) ;
+ if (bound == fabs(params[itype].qform)) continue;
+ if (fabs(q[i]) < bound) test[gp] = 1;
+ }
+ }
+
+ MPI_Allreduce(test,init,nteam+1,MPI_INT,MPI_SUM,world);
+
+ // On fait que sur les atomes hybrides!!!
+ // ----------------------------------------
+
+ tot = totll = 0.0;
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii]; itype = map[type[i]];
+ gp = flag_QEq[i];
+
+ if (gp != 0 && init[gp] != 0) {
+ if (itype == 0) q[i] = -1.96;
+ if (itype != 0) q[i] = 1.96 * double(nQEqaall[gp]) / double(nQEqcall[gp]);
+ }
+ tot += q[i];
+ }
+ MPI_Allreduce(&tot,&totll,1,MPI_INT,MPI_SUM,world);
+ if (me == 0) printf (" === Fin de init_charge qtot %20.15f ====\n",totll);
+
+}
+/* ----------------------------------------------------------------------
+ * COMMUNICATION
+ * ---------------------------------------------------------------------- */
+
+int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i ++) {
+ j = list[i];
+ buf[m++] = tab_comm[j];
+// if (j < 3) printf ("[%d] %d pfc %d %d buf_send = %f \n",me,n,i,m-1,buf[m-1]);
+ }
+ return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n ;
+ for (i = first; i < last; i++) {
+ tab_comm[i] = buf[m++];
+// if (i<first+3) printf ("[%d] ufc %d %d buf_recv = %f \n",me,i,m-1,buf[m-1]);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int PairSMTBQ::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = tab_comm[i];
+// if (i<first+3) printf ("[%d] prc %d %d buf_send = %f \n",me,i,m-1,buf[m-1]);
+ }
+ return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ // tab_comm[j] += buf[m++];
+ tab_comm[j] = buf[m++];
+// if (j<3) printf ("[%d] %d urc %d %d buf_recv = %f \n",me,n,i,m-1,buf[m-1]);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::forward(double *tab)
+{
+ int i;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+
+ for (i=0; i<nlocal+nghost; i++) tab_comm[i] = tab[i];
+
+ comm->forward_comm_pair(this);
+
+ for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::reverse(double *tab)
+{
+ int i;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+
+ for (i=0; i<nlocal+nghost; i++) tab_comm[i] = tab[i];
+
+ comm->reverse_comm_pair(this);
+
+ for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::forward_int(int *tab)
+{
+ int i;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+
+ for (i=0; i<nlocal+nghost; i++) { tab_comm[i] = double(tab[i]);}
+
+ comm->forward_comm_pair(this);
+
+ for (i=0; i<nlocal+nghost; i++) {
+ if (fabs(tab_comm[i]) > 0.1) tab[i] = int(tab_comm[i]) ; }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::reverse_int(int *tab)
+{
+ int i;
+ int nlocal = atom->nlocal;
+ int nghost = atom->nghost;
+
+ for (i=0; i<nlocal+nghost; i++) { tab_comm[i] = double(tab[i]);}
+
+ comm->reverse_comm_pair(this);
+
+ for (i=0; i<nlocal+nghost; i++) {
+ if (fabs(tab_comm[i]) > 0.1) tab[i] = int(tab_comm[i]); }
+}
+
+/* ---------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+double PairSMTBQ::memory_usage()
+{
+ double bytes = maxeatom * sizeof(double);
+ bytes += maxvatom*6 * sizeof(double);
+ bytes += nmax * sizeof(int);
+ bytes += MAXNEIGH * nmax * sizeof(int);
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSMTBQ::add_pages(int howmany)
+{
+ int toppage = maxpage;
+ maxpage += howmany*PGDELTA;
+
+ pages = (int **)
+ memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages");
+ for (int i = toppage; i < maxpage; i++)
+ memory->create(pages[i],pgsize,"pair:pages[i]");
+}
+
+/* ---------------------------------------------------------------------- */
+
+
+int PairSMTBQ::Tokenize( char* s, char*** tok )
+{
+ char test[MAXLINE];
+ const char *sep = "' ";
+ char *mot;
+ int count=0;
+ mot = NULL;
+
+
+ strncpy( test, s, MAXLINE );
+
+ for( mot = strtok(test, sep); mot; mot = strtok(NULL, sep) ) {
+ strncpy( (*tok)[count], mot, MAXLINE );
+ count++;
+ }
+
+ return count;
+}
+
+
+
+void PairSMTBQ::CheckEnergyVSForce()
+{
+ double drL,iq,jq,rsq,evdwlCoul,fpairCoul,eflag,ErepR,frepR,fpair,evdwl;
+ int i,j,iiiMax,iii,iCoord;
+ int itype,jtype,l,m;
+ double r,t1,t2,sds,xi,engSurf,fforceSurf;
+ double eng,fforce,engBB,fforceBB;
+
+ double za,zb,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
+ int *type = atom->type;
+ char *NameFile;
+
+
+ i=0;
+ j=1;
+ map[type[i]]=0; //ox
+ itype=map[type[i]];
+ iq=-1;
+
+
+ map[type[j]]=0; //ox
+ jtype=map[type[j]];
+ jq=-1;
+ coord[i]=coordOxBulk;
+ coord[j]=coordOxBulk;
+ m = intype[itype][jtype];
+
+
+ na = params[itype].ne ;
+ nb = params[jtype].ne ;
+ za = params[itype].dzeta ;
+ zb = params[jtype].dzeta ;
+
+
+ // Ouverture du fichier
+
+ for (iCoord=1;iCoord<5; iCoord++)
+ {
+
+ if (iCoord==1)
+ {coord[i]=2.2;
+ coord[j]=2.1;
+ NameFile="energyandForceOxOxUnderCoord.txt";
+ }
+ if (iCoord==2)
+ {coord[i]=coordOxBulk;
+ coord[j]=coordOxBulk;
+ NameFile="energyandForceOxOxCoordBulk.txt";
+ }
+ if (iCoord==3)
+ {coord[i]=3.8;
+ coord[j]=4;
+ NameFile="energyandForceOxOxOverCoord.txt";
+ }
+ if (iCoord==4)
+ {coord[i]=2.2;
+ coord[j]=3.5;
+ NameFile="energyandForceOxOxUnderOverCoord.txt";
+ }
+
+
+ ofstream fichierOxOx(NameFile, ios::out | ios::trunc) ;
+
+ drL=0.0001;
+ iiiMax=int((cutmax-1.2)/drL);
+ for (iii=1; iii< iiiMax ; iii++){
+ r=1.2+drL*iii;
+ rsq=r*r;
+ evdwlCoul = 0.0 ; fpairCoul = 0.0;
+ potqeq(i,j,iq,jq,rsq,fpairCoul,eflag,evdwlCoul);
+ fpairCoul=fpairCoul*r;
+
+ rep_OO (&intparams[m],rsq,fpair,eflag,evdwl);
+ ErepR = evdwl;
+ frepR= fpair*r;
+
+ gam = dgam = dza = dzb = d2zaa = d2zab =
+ d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
+
+
+// gammas_(na,nb,za,zb,r,gam,dgam,dza,dzb,
+// d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+ gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+
+
+ sds = rsq/ds ; l = int(sds) ;
+ xi = sds - double(l) ;
+
+
+ t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
+ t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
+ eng = iq*jq*(t1 + (t2 - t1)*xi/2.0);
+
+ t1 = dfafb[l][m] + (dfafb[l+1][m] - dfafb[l][m])*xi;
+ t2 = dfafb[l+1][m] + (dfafb[l+2][m] - dfafb[l+1][m])*(xi-1);
+ fforce = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ;
+
+
+ t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi;
+ t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0);
+ engSurf = iq*jq*(t1 + (t2 - t1)*xi/2.0);
+
+ t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi;
+ t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0);
+ engBB = iq*jq*(t1 + (t2 - t1)*xi/2.0);
+
+ t1 = dfafbOxOxSurf[l] + (dfafbOxOxSurf[l+1] - dfafbOxOxSurf[l])*xi;
+ t2 = dfafbOxOxSurf[l+1] + (dfafbOxOxSurf[l+2] - dfafbOxOxSurf[l+1])*(xi-1);
+ fforceSurf = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ;
+
+ t1 = dfafbOxOxBB[l] + (dfafbOxOxBB[l+1] - dfafbOxOxBB[l])*xi;
+ t2 = dfafbOxOxBB[l+1] + (dfafbOxOxBB[l+2] - dfafbOxOxBB[l+1])*(xi-1);
+ fforceBB = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ;
+
+ if (fichierOxOx) { fichierOxOx<< setprecision (9) <<r <<" "<<evdwlCoul <<" " <<fpairCoul <<" "<<eng <<" " <<fforce <<" "<<engSurf <<" " <<fforceSurf <<" "<<engBB <<" " <<fforceBB <<" "<<ErepR<<" "<<frepR<<" "<<gam<<" "<<dgam<<endl ;}
+
+ }
+
+
+ if (fichierOxOx) fichierOxOx.close() ;
+ }
+
+
+
+ map[type[j]]=1; //met
+ jtype=map[type[j]];
+ jq=1;
+ coord[i]=coordOxBulk;
+ coord[j]=6;
+ m = intype[itype][jtype];
+
+
+ na = params[itype].ne ;
+ nb = params[jtype].ne ;
+ za = params[itype].dzeta ;
+ zb = params[jtype].dzeta ;
+
+
+ // Ouverture du fichier
+
+ for (iCoord=1;iCoord<4; iCoord++)
+ {
+
+ if (iCoord==1)
+ {coord[i]=2.2;
+ coord[j]=2.1;
+ NameFile="energyandForceOxTiUnderCoord.txt";
+ }
+ if (iCoord==2)
+ {coord[i]=coordOxBulk;
+ coord[j]=coordOxBulk;
+ NameFile="energyandForceOxTiCoordBulk.txt";
+ }
+ if (iCoord==3)
+ {coord[i]=3.8;
+ coord[j]=4;
+ NameFile="energyandForceOxTiOverCoord.txt";
+ }
+
+
+ ofstream fichierOxTi(NameFile, ios::out | ios::trunc) ;
+
+ drL=0.0001;
+ iiiMax=int((cutmax-1.2)/drL);
+ for (iii=1; iii< iiiMax ; iii++){
+ r=1.2+drL*iii;
+ rsq=r*r;
+ evdwlCoul = 0.0 ; fpairCoul = 0.0;
+ potqeq(i,j,iq,jq,rsq,fpairCoul,eflag,evdwlCoul);
+ fpairCoul=fpairCoul*r;
+
+ rep_OO (&intparams[m],rsq,fpair,eflag,evdwl);
+ ErepR = evdwl;
+ frepR= fpair*r;
+
+ gam = dgam = dza = dzb = d2zaa = d2zab =
+ d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
+
+
+// gammas_(na,nb,za,zb,r,gam,dgam,dza,dzb,
+// d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+ gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
+
+
+ if (fichierOxTi) { fichierOxTi<< setprecision (9) <<r <<" "<<evdwlCoul <<" " <<fpairCoul <<" "<<ErepR<<" "<<frepR<<" "<<gam<<" "<<dgam<<endl ;}
+
+ }
+
+
+ if (fichierOxTi) fichierOxTi.close() ;
+ }
+
+ exit(0);
+}
+
+/* :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+ GAMMAS FUNCTION (GALE)
+ ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: */
+
+void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r, double &gam,
+ double &dgam, double &dza, double &dzb, double &d2zaa, double &d2zab, double &d2zbb,
+ double &d2zra, double &d2zrb, double &d2gamr2)
+{
+/* ---------------------------------------------------------------
+ Subroutine calculates the integral over two s orbtials
+ for Slater functions
+
+ On input :
+
+ na = principle quantum number of A
+ nb = principle quantum number of B
+ za = orbital exponent of A
+ zb = orbital exponent of B
+ r = distance between A and B
+
+ On exit :
+
+ gam = integral
+ dgam = first derivative of gam with respect to r
+ dza = first derivative of gam with respect to za
+ dzb = first derivative of gam with respect to zb
+ d2zaa = second derivative of gam with respect to za/za
+ d2zab = second derivative of gam with respect to za/zb
+ d2zbb = second derivative of gam with respect to zb/zb
+ d2zra = second derivative of gam with respect to r/za
+ d2zrb = second derivative of gam with respect to r/zb
+ d2gamr2 = second derivative of gam with respect to r
+
+ Julian Gale, Imperial College, December 1997
+ ---------------------------------------------------------------- */
+
+ int i;
+ double z2ra,z2rb,na2,nb2,halfr,d2rtm,drtrm,rtrm,ss,deriv,
+ dzeta1,dzeta2,d2zeta11,d2zeta12,d2zeta22,d2zeta1r,
+ d2zeta2r,deriv2,trm1,trm2,trm3,d2rtrm,ztrm,ctrm,
+ rfct1,rgam1,rdza1,rgam2;
+
+
+
+ gam=0.0;
+ dgam=0.0;
+ dza=0.0;
+ dzb=0.0;
+ d2zaa=0.0;
+ d2zab=0.0;
+ d2zbb=0.0;
+ d2zra=0.0;
+ d2zrb=0.0;
+ d2gamr2=0.0;
+
+// This routine only handles two centre integrals
+
+
+ if (r < 1.0e-10) return;
+
+
+// Create local variables
+
+ z2ra=2.0*za*r;
+ z2rb=2.0*zb*r;
+ na2=2*na;
+ nb2=2*nb;
+ halfr=0.5*r;
+ d2rtrm=pow(halfr,na2-2);
+ drtrm=d2rtrm*halfr;
+ rtrm=drtrm*halfr;
+
+// First term
+
+
+ css(ss,na2-1,0,z2ra,0.0,r,deriv,dzeta1,dzeta2,
+ d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,
+ deriv2) ;
+
+ gam=rtrm*ss;
+ dgam=rtrm*deriv+float(na)*drtrm*ss;
+ dza=rtrm*dzeta1;
+ d2zaa=rtrm*d2zeta11;
+ d2zra=rtrm*d2zeta1r+float(na)*drtrm*dzeta1;
+ d2gamr2=d2gamr2+0.5*float(na*(na2-1))*d2rtrm*ss + 2.0*float(na)*drtrm*deriv+rtrm*deriv2;
+
+// Sum over 2*nb
+
+ rtrm=drtrm;
+ drtrm=d2rtrm;
+ ztrm=0.5/(zb*float(nb2));
+
+ for (i = nb2; i >= 1; i--) {
+ rtrm=rtrm*halfr;
+ drtrm=drtrm*halfr;
+ ztrm=ztrm*2.0*zb;
+ ctrm=ztrm/factorial(nb2-i);
+
+ css(ss,na2-1,nb2-i,z2ra,z2rb,r,deriv,dzeta1,dzeta2,
+ d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,deriv2);
+
+ trm1=float(i)*ctrm;
+ trm2=trm1*rtrm;
+ gam=gam-trm2*ss;
+ trm3=trm1*float(na2+nb2-i)*drtrm;
+ dgam=dgam-trm2*deriv-0.5*trm3*ss;
+ d2gamr2=d2gamr2-trm2*deriv2-trm3*deriv-0.5*trm3*float(na2+nb2-i-1)*ss/r;
+ dza=dza-trm2*dzeta1;
+ dzb=dzb-(trm2/zb)*((float(nb2-i))*ss+zb*dzeta2);
+ d2zaa=d2zaa-trm2*d2zeta11;
+ d2zab=d2zab-(trm2/zb)*((float(nb2-i))*dzeta1+zb*d2zeta12);
+ d2zbb=d2zbb-(trm2/zb)*(2.0*(float(nb2-i))*dzeta2+zb*d2zeta22 +
+ (float((nb2-i-1)*(nb2-i))*ss/zb));
+ d2zra=d2zra-trm2*d2zeta1r-0.5*trm3*dzeta1;
+ d2zrb=d2zrb-(trm2/zb)*((float(nb2-i))*deriv+zb*d2zeta2r) -
+ 0.5*(trm3/zb)*((float(nb2-i))*ss+zb*dzeta2);
+ }
+
+// Multiply by coefficients
+
+ trm3=pow(2.0*za,na2+1)/factorial(na2);
+ gam=gam*trm3;
+ dgam=dgam*trm3;
+ rfct1=((float(na2+1))/za);
+ rgam1=rfct1*gam;
+ dza=dza*trm3;
+ rdza1=2.0*rfct1*dza;
+ dza=dza+rgam1;
+ dzb=dzb*trm3;
+ rgam2=rgam1*float(na2)/za;
+ d2zaa=d2zaa*trm3+rgam2+rdza1;
+ d2zab=d2zab*trm3+rfct1*dzb;
+ d2zbb=d2zbb*trm3;
+ d2zra=d2zra*trm3+rfct1*dgam;
+ d2zrb=d2zrb*trm3;
+ d2gamr2=d2gamr2*trm3;
+ return;
+
+ }
+/* --------------------------------------------------------------------------------
+ Css
+ -------------------------------------------------------------------------------- */
+void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta, double r,
+ double &deriv, double &dzeta1, double &dzeta2, double &d2zeta11, double &d2zeta12,
+ double &d2zeta22, double &d2zeta1r, double &d2zeta2r, double &deriv2)
+{
+// implicit real (a-h,o-z)
+// common /fctrl/ fct(30) // A RAJOUTER DANS Pair_SMTBQ.h
+/* ------------------------------------------------------------------
+ Modified integral calculation routine for Slater orbitals
+ including derivatives. This version is for S orbitals only.
+
+ dzeta1 and dzeta2 are the first derivatives with respect to zetas
+ and d2zeta11/d2zeta12/d2zeta22 are the second.
+ d2zeta1r and d2zeta2r are the mixed zeta/r second derivatives
+ deriv2 is the second derivative with respect to r
+
+ Julian Gale, Imperial College, December 1997
+ ------------------------------------------------------------------- */
+ int i,i1,nni1; //ulim
+ double ulim,n1,n2,p,pt,x,k,dpdz1,dpdz2,dptdz1,dptdz2,dpdr,dptdr,d2pdz1r,
+ d2pdz2r,d2ptdz1r,d2ptdz2r,zeta1,zeta2,sumzeta,difzeta,coff;
+
+ double da1[30],da2[30],db1[30],db2[30];
+ double d2a11[30],d2a12[30],d2a22[30],dar[30];
+ double d2b11[30],d2b12[30],d2b22[30],dbr[30];
+ double d2a1r[30],d2a2r[30],d2b1r[30],d2b2r[30];
+ double d2ar2[30],d2br2[30];
+
+ double *a,*b;
+ memory->create(a,31,"pair:a");
+ memory->create(b,31,"pair:a");
+
+
+// Set up factorials - stored as factorial(n) in location(n+1)
+
+ for (i = 1; i <= 30; i++) {
+ fct[i]=factorial(i-1);
+ }
+ dzeta1=0.0;
+ dzeta2=0.0;
+ d2zeta11=0.0;
+ d2zeta12=0.0;
+ d2zeta22=0.0;
+ d2zeta1r=0.0;
+ d2zeta2r=0.0;
+ deriv=0.0;
+ deriv2=0.0;
+ n1=nn1;
+ n2=nn2;
+ p =(alpha + beta)*0.5;
+ pt=(alpha - beta)*0.5;
+ x = 0.0;
+ zeta1=alpha/r;
+ zeta2=beta/r;
+ sumzeta=zeta1+zeta2;
+ difzeta=zeta1-zeta2;
+
+// Partial derivative terms for zeta derivatives
+
+ dpdz1=r;
+ dpdz2=r;
+ dptdz1=r;
+ dptdz2=-r;
+ dpdr=0.5*sumzeta;
+ dptdr=0.5*difzeta;
+ d2pdz1r=1.0;
+ d2pdz2r=1.0;
+ d2ptdz1r=1.0;
+ d2ptdz2r=-1.0;
+
+// Reverse quantum numbers if necessary -
+// also change the sign of difzeta to match
+// change in sign of pt
+
+ if (n2 < n1) {
+ k = n1;
+ n1= n2;
+ n2= k;
+ pt=-pt;
+ difzeta=-difzeta;
+ dptdr=-dptdr;
+ dptdz1=-dptdz1;
+ dptdz2=-dptdz2;
+ d2ptdz1r=-d2ptdz1r;
+ d2ptdz2r=-d2ptdz2r;
+ }
+
+// Trap for enormously long distances which would cause
+// caintgs or cbintgs to crash with an overflow
+
+ if (p > 86.0 || pt > 86.0) {
+ s=0.0;
+ return;
+ }
+//***************************
+// Find a and b integrals *
+//***************************
+ caintgs(p,n1+n2+3,a);
+ cbintgs(pt,n1+n2+3,b);
+
+// Convert derivatives with respect to p and pt
+// into derivatives with respect to zeta1 and
+// zeta2
+
+ ulim=n1+n2+1;
+ for (i = 1; i <= int(ulim); i++) {
+ da1[i]=-a[i+1]*dpdz1;
+ da2[i]=-a[i+1]*dpdz2;
+ db1[i]=-b[i+1]*dptdz1;
+ db2[i]=-b[i+1]*dptdz2;
+ d2a11[i]=a[i+2]*dpdz1*dpdz1;
+ d2a12[i]=a[i+2]*dpdz1*dpdz2;
+ d2a22[i]=a[i+2]*dpdz2*dpdz2;
+ d2b11[i]=b[i+2]*dptdz1*dptdz1;
+ d2b12[i]=b[i+2]*dptdz1*dptdz2;
+ d2b22[i]=b[i+2]*dptdz2*dptdz2;
+ dar[i]=-a[i+1]*dpdr;
+ dbr[i]=-b[i+1]*dptdr;
+ d2a1r[i]=a[i+2]*dpdz1*dpdr-a[i+1]*d2pdz1r;
+ d2a2r[i]=a[i+2]*dpdz2*dpdr-a[i+1]*d2pdz2r;
+ d2b1r[i]=b[i+2]*dptdz1*dptdr-b[i+1]*d2ptdz1r;
+ d2b2r[i]=b[i+2]*dptdz2*dptdr-b[i+1]*d2ptdz2r;
+ d2ar2[i]=a[i+2]*dpdr*dpdr;
+ d2br2[i]=b[i+2]*dptdr*dptdr;
+ }
+
+// Begin section used for overlap integrals involving s functions
+
+ for (i1 = 1; i1 <= int(ulim); i1++) {
+ nni1=n1+n2-i1+2;
+ coff=coeffs(n1,n2,i1-1);
+ deriv=deriv+coff*(dar[i1]*b[nni1]+a[i1]*dbr[nni1]);
+ x=x+coff*a[i1]*b[nni1];
+ dzeta1=dzeta1+coff*(da1[i1]*b[nni1]+a[i1]*db1[nni1]);
+ dzeta2=dzeta2+coff*(da2[i1]*b[nni1]+a[i1]*db2[nni1]);
+ d2zeta11=d2zeta11+coff*(d2a11[i1]*b[nni1]+a[i1]*d2b11[nni1]+
+ 2.0*da1[i1]*db1[nni1]);
+ d2zeta12=d2zeta12+coff*(d2a12[i1]*b[nni1]+a[i1]*d2b12[nni1]+
+ da1[i1]*db2[nni1]+da2[i1]*db1[nni1]);
+ d2zeta22=d2zeta22+coff*(d2a22[i1]*b[nni1]+a[i1]*d2b22[nni1]+
+ 2.0*da2[i1]*db2[nni1]);
+ d2zeta1r=d2zeta1r+coff*(d2a1r[i1]*b[nni1]+dar[i1]*db1[nni1]+
+ da1[i1]*dbr[nni1]+a[i1]*d2b1r[nni1]);
+ d2zeta2r=d2zeta2r+coff*(d2a2r[i1]*b[nni1]+dar[i1]*db2[nni1]+
+ da2[i1]*dbr[nni1]+a[i1]*d2b2r[nni1]);
+ deriv2=deriv2+coff*(d2ar2[i1]*b[nni1]+a[i1]*d2br2[nni1]+
+ 2.0*dar[i1]*dbr[nni1]);
+ }
+ s=x*0.5;
+ deriv=0.5*deriv;
+ deriv2=0.5*deriv2;
+ dzeta1=0.5*dzeta1;
+ dzeta2=0.5*dzeta2;
+ d2zeta11=0.5*d2zeta11;
+ d2zeta12=0.5*d2zeta12;
+ d2zeta22=0.5*d2zeta22;
+ d2zeta1r=0.5*d2zeta1r;
+ d2zeta2r=0.5*d2zeta2r;
+
+ memory->destroy(a);
+ memory->destroy(b);
+
+ return;
+}
+/* -------------------------------------------------------------------------------
+ coeffs
+ ------------------------------------------------------------------------------- */
+ double PairSMTBQ::coeffs(int na, int nb, int k)
+ {
+ // implicit real (a-h,o-z)
+ // common /fctrl/ fct(30)
+
+ int il,lie,je,ia,i,j,ie,l;
+ double coeffs;
+
+// Statement function
+// binm(n,i)=fct(n+1)/(fct(n-i+1)*fct(i+1));
+
+ coeffs=0.0;
+ l=na+nb-k;
+ ie=min(l,na)+1;
+ je=min(l,nb);
+ ia=l-je+1;
+ for (il = ia; il <= ie; il++) {
+ i=il-1;
+ j=l-i; // D'ou vient le i
+ coeffs=coeffs + binm(na,i)*binm(nb,j)*pow(-1.,j);
+ }
+ return coeffs;
+ }
+
+// ============================================
+
+double PairSMTBQ::binm(int n, int i)
+{
+ return fct[n+1]/(fct[n-i+1]*fct[i+1]);
+}
+
+/* ---------------------------------------------------------------------------------
+ Caintgs
+ -------------------------------------------------------------------------------- */
+ void PairSMTBQ::caintgs (double x, int k, double *a)
+ {
+// implicit real (a-h,o-z)
+// dimension a(30)
+ int i;
+ double cste,rx;
+
+ cste=exp(-x);
+ rx=1.0/x;
+ a[1]=cste*rx;
+ for (i = 1; i <= k; i++) {
+ a[i+1]=(a[i]*float(i)+cste)*rx;
+ }
+ return;
+ }
+/* -----------------------------------------------------------------------------------
+ Cbintgs
+ ----------------------------------------------------------------------------------- */
+void PairSMTBQ::cbintgs( double x, int k, double *b)
+{
+// implicit real (a-h,o-z)
+/* *******************************************************************
+! Fills array of b-integrals. note that b(i) is b(i-1) in the
+! usual notation
+! for x.gt.3 exponential formula is used
+! for 2.lt.x.le.3 and k.le.10 exponential formula is used
+! for 2.lt.x.le.3 and k.gt.10 15 term series is used
+! for 1.lt.x .e.2 and k.le.7 exponential formula is used
+! for 1.lt.x.le.2 and k.gt.7 12 term series is used
+! for .5.lt.x.le.1 and k.le.5 exponential formula is used
+! for .5.lt.x.le.1 and k.gt.5 7 term series is used
+! for x.le..5 6 term series is used
+!******************************************************************* */
+// dimension b(30)
+// common /fctrl/ fct(30)
+
+ int i0,m,last,i;
+ double absx,expx,expmx,ytrm,y,rx;
+
+ i0=0;
+ absx=fabs(x);
+
+ if (absx > 3.0) goto g120;
+ if (absx > 2.0) goto g20;
+ if (absx > 1.0) goto g50;
+ if (absx > 0.5) goto g80;
+ if (absx > 1.0e-8) goto g110;
+ goto g170;
+ g110: last=6;
+ goto g140;
+ g80: if (k <= 5) goto g120;
+ last=7;
+ goto g140;
+ g50: if (k <= 7) goto g120;
+ last=12;
+ goto g140;
+ g20: if (k <= 10) goto g120;
+ last=15;
+ goto g140;
+
+ g120: expx=exp(x);
+ expmx=1./expx;
+ rx=1.0/x;
+ b[1]=(expx-expmx)*rx;
+ for (i = 1; i <= k ; i++) {
+ b[i+1]=(float(i)*b[i]+ pow(-1.0,i)*expx-expmx)*rx;
+ }
+ goto g190;
+//
+// Series to calculate b(i)
+//
+ g140: for (i = i0; i <= k ; i++) {
+ y=0.;
+ for (m = i0; m <= last; m++) {
+ ytrm = pow(-x,m-1)*(1. - pow(-1.,m+i+1))/(fct[m+1]*float(m+i+1));
+ y = y + ytrm*(-x);
+ }
+ b[i+1] = y;
+ }
+ goto g190;
+//
+// x extremely small
+//
+ g170: for (i = i0; i <= k; i++) {
+ b[i+1] = (1.-pow(-1.,i+1))/float(i+1);
+ }
+ g190:
+ return;
+ }
+/* ------------------------------------------------------------------------------------
+ Factorial
+ ------------------------------------------------------------------------------------ */
+double PairSMTBQ::factorial(double n)
+{
+// implicit real(a-h,o-z)
+ double rn,factorial;
+ int i;
+
+//
+// Calculates the factorial of an integer n
+//
+ rn = n;
+ if (n <= 1.) {
+ factorial=1.0;
+ return factorial;
+ }
+ factorial=1.0;
+ for (i = 2; i <= int(n); i++) {
+ factorial = factorial*float(i);
+ }
+ return factorial;
+}
+
+
+/* ============================== This is the END... ================================== */
diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h
new file mode 100644
index 000000000..2a1dc3bb8
--- /dev/null
+++ b/src/USER-SMTBQ/pair_smtbq.h
@@ -0,0 +1,197 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(smtbq,PairSMTBQ)
+
+#else
+
+#ifndef LMP_PAIR_SMTBQ_H
+#define LMP_PAIR_SMTBQ_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairSMTBQ : public Pair {
+ public:
+ PairSMTBQ(class LAMMPS *);
+ virtual ~PairSMTBQ();
+ virtual void compute(int, int);
+
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ double init_one(int, int);
+ double memory_usage();
+
+
+protected:
+ struct Param {
+ double sto,n0,ne,chi,dj;
+ double R,dzeta; //Rayon slater
+ double cutsq;
+ double qform, masse; // Charge formelle
+ char *nom;
+ };
+
+ struct Intparam {
+ double a,p,ksi,q,r0,dc1,dc2;
+ double abuck,rhobuck,neig_cut,aOO,bOO,r1OO,r2OO;
+ char *typepot,*mode;
+ int intsm;
+ };
+
+ double rmin,dr,ds; // table parameter
+ int kmax;
+ int Qstep; // Frenquence of charge resolution
+ double precision; // acurate of convergence
+ int loopmax; // max of interation
+
+ double cutmax; // max cutoff for all elements
+ int nelements; // # of unique elements
+ char **elements; // names of unique elements
+ char *QEqMode; // name of QEqMode
+ char *Bavard; // Verbose parameter
+ char *writepot; // write or not the electronegativity component
+ char *writeenerg; // write or not the energy component
+ char *QInitMode; // mode of initialization of charges
+ double zlim1QEq; // z limit for QEq equilibration
+ double zlim2QEq; // z limit for QEq equilibration
+ double QOxInit; // Initial charge for oxygen atoms (if the charge is not specified)
+ int *map; // mapping from atom types to elements
+ int nparams; // # of stored parameter sets
+ int maxparam; // max # of parameter sets
+ int maxintparam; // max # of interaction sets
+ int maxintsm; // max # of interaction SM
+ double r1Coord,r2Coord;
+ Param *params; // parameter set for an I atom
+ Intparam *intparams; // parameter set for an I interaction
+
+ int nmax,*nQEqall,*nQEqaall,*nQEqcall;
+ double *qf,*q1,*q2,Nevery,Neverypot;
+
+// Coulombian interaction
+ double *esm, **fafb, **dfafb, *fafbOxOxSurf, *dfafbOxOxSurf, *fafbTiOxSurf,*dfafbTiOxSurf;
+ double *potqn, *dpotqn, Vself, *Zsm,*coord, *fafbOxOxBB, *dfafbOxOxBB,*fafbTiOxBB, *dfafbTiOxBB ;
+ int **intype, **coultype;
+ int *NCo;
+ double coordOxBulk,coordOxSurf,ROxSurf,coordOxBB,ROxBB;
+
+// Covalent interaction
+ double *ecov, *potmad, *potself, *potcov, *chimet;
+ double **tabsmb,**dtabsmb, **tabsmr, **dtabsmr, *sbcov, *sbmet;
+ double ncov;
+
+// Neighbor Table
+ int nteam,cluster,*hybrid;
+ int *nvsm, **vsm, *flag_QEq;
+
+// Parallelisation
+ int me, nproc;
+ double *tab_comm;
+
+// GAMMAS function
+ double *fct;
+
+// HERE its routines
+// =====================================
+ void allocate();
+ virtual void read_file(char *);
+
+ void tabsm();
+ void tabqeq();
+
+ void potqeq(int, int, double, double, double,
+ double &, int, double &);
+ void pot_ES (int, int, double, double &);
+ void pot_ES2 (int, int, double, double &);
+
+ double self(Param *, double);
+ double qfo_self(Param *, double);
+
+ virtual void repulsive(Intparam *, double, int, int, double &, int, double &);
+ virtual void rep_OO (Intparam *, double, double &, int, double &);
+ virtual void Attr_OO (Intparam *, double, double &, int, double &);
+ virtual void attractive(Intparam *, double, int, int, double, int, double );
+ void f_att(Intparam *, int, int, double, double &) ;
+ void pot_COV(Param *, int, double &);
+ double potmet(Intparam *, double, int, double, int, double);
+
+ double fcoupure(double, double, double);
+ double fcoupured(double, double, double);
+
+ double fcoup2(double, double, double);
+ double Intfcoup2(double, double, double);
+ double Primfcoup2(double, double, double);
+
+ void groupBulkFromSlab_QEq();
+ void groupQEqAllParallel_QEq();
+ void groupQEqAll_QEq();
+ void groupSurface_QEq();
+ void QForce_charge(int);
+ void Charge();
+ void Init_charge(int*, int*, int*);
+ void CheckEnergyVSForce();
+
+// ===========================================
+// Communication pack
+ int pack_forward_comm (int, int*, double*, int, int*);
+ void unpack_forward_comm (int, int, double*);
+ int pack_reverse_comm (int, int, double*);
+ void unpack_reverse_comm (int, int*, double*);
+ void forward (double*); void reverse (double*);
+ void forward_int (int*); void reverse_int (int*);
+
+ int Tokenize( char* , char*** );
+
+ inline double vec3_dot(const double x[3], const double y[3]) const {
+ return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
+ }
+
+ template <class T> const T& min ( const T& a, const T& b ) {
+ return !(b<a)?a:b; // or: return !comp(b,a)?a:b; for the comp version
+ }
+
+// =============================================
+// Gammas function
+ void gammas(double &, double &, double &, double &, double &, double &,
+ double &, double &, double &, double &, double &, double &,
+ double &, double &, double &);
+
+ void css(double &, double, double, double, double, double,
+ double &, double &, double &, double &,double &,
+ double &, double &, double &, double &);
+
+ double coeffs(int, int, int);
+
+ double binm(int, int);
+ void caintgs (double, int, double *);
+ void cbintgs( double, int, double *);
+ double factorial(double);
+
+
+// =====================================
+// short range neighbor list
+
+ void add_pages(int howmany = 1);
+// void Short_neigh();
+ int maxpage, pgsize, oneatom, **pages;
+ double cutmin;
+};
+
+}
+
+#endif
+#endif
diff --git a/src/version.h b/src/version.h
index 6439ed804..d2dd60a0c 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "23 Oct 2015"
+#define LAMMPS_VERSION "24 Oct 2015"