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<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="10 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<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>10 Aug 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A 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>

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@ -1067,70 +1067,70 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<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.html"><em>lj/cut (cgikot)</em></a></td>
<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>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long (cgikot)</em></a></td>
<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/msm (go)</em></a></td>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/cut (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs/coul/gromacs (cko)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_smooth.html"><em>lj/smooth (co)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><em>lubricate/poly (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_mie.html"><em>mie/cut (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/cut (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/pmb (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_airebo.html"><em>rebo (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
<tr class="row-odd"><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>
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cko)</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.html"><em>tersoff (cgko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
<td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
<td><a class="reference internal" href="pair_zbl.html"><em>zbl (o)</em></a></td>
<td>&nbsp;</td>
<td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
</tr>
</tbody>
</table>

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View File

@ -832,6 +832,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"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,
@ -874,7 +875,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"soft (go)"_pair_soft.html,
"sw (cgkio)"_pair_sw.html,
"table (gko)"_pair_table.html,
"tersoff (cko)"_pair_tersoff.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,
@ -882,7 +883,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"tri/lj (o)"_pair_tri_lj.html,
"yukawa (go)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (o)"_pair_zbl.html :tb(c=4,ea=c)
"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

17
doc/Section_start.html
View File

@ -395,8 +395,18 @@ within the LAMMPS code. The options that are currently recogized are:</p>
</ul>
<p>The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your machine supports
the &#8220;popen&#8221; function in the standard runtime library and that a gzip
the &#8220;popen()&#8221; function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
provided in the COMPRESS package. From more details about compiling
LAMMPS with packages, please see below.</p>
</div>
<p>If you use -DLAMMPS_JPEG, the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command
will be able to write out JPEG image files. For JPEG files, you must
also link LAMMPS with a JPEG library, as described below. If you use
@ -410,6 +420,11 @@ will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your
machines supports the &#8220;popen&#8221; function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().</p>
</div>
<p>Using -DLAMMPS_MEMALIGN=&lt;bytes&gt; enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
are allocated by LAMMPS. This can help to make more efficient use of

13
doc/Section_start.txt
View File

@ -266,9 +266,17 @@ within the LAMMPS code. The options that are currently recogized are:
The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your machine supports
the "popen" function in the standard runtime library and that a gzip
the "popen()" function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.
IMPORTANT NOTE: on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
provided in the COMPRESS package. From more details about compiling
LAMMPS with packages, please see below.
If you use -DLAMMPS_JPEG, the "dump image"_dump_image.html command
will be able to write out JPEG image files. For JPEG files, you must
also link LAMMPS with a JPEG library, as described below. If you use
@ -284,6 +292,9 @@ the need to store intermediate image files. It requires that your
machines supports the "popen" function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.
IMPORTANT NOTE: Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().
Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
are allocated by LAMMPS. This can help to make more efficient use of

38
doc/dump.html
View File

@ -127,6 +127,9 @@
<div class="section" id="dump-command">
<span id="index-0"></span><h1>dump command<a class="headerlink" href="#dump-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dump-h5md-command">
<h1><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command<a class="headerlink" href="#dump-h5md-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dump-image-command">
<h1><a class="reference internal" href="dump_image.html"><em>dump image</em></a> command<a class="headerlink" href="#dump-image-command" title="Permalink to this headline"></a></h1>
</div>
@ -143,24 +146,32 @@
<ul class="simple">
<li>ID = user-assigned name for the dump</li>
<li>group-ID = ID of the group of atoms to be dumped</li>
<li>style = <em>atom</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/mpiio</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/mpiio</em></li>
<li>style = <em>atom</em> or <em>atom/gz</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/gz</em> or <em>xyz/mpiio</em> or <em>h5md</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em></li>
<li>N = dump every this many timesteps</li>
<li>file = name of file to write dump info to</li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>atom</em> args = none
<em>atom/gz</em> args = none
<em>atom/mpiio</em> args = none
<em>cfg</em> args = same as <em>custom</em> args, see below
<em>cfg/gz</em> args = same as <em>custom</em> args, see below
<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
<em>dcd</em> args = none
<em>xtc</em> args = none
<em>xyz</em> args = none
</pre>
<pre class="literal-block">
<em>xyz/gz</em> args = none
</pre>
<pre class="literal-block">
<em>xyz/mpiio</em> args = none
</pre>
<pre class="literal-block">
<em>h5md</em> args = discussed on <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> doc page
</pre>
<pre class="literal-block">
<em>image</em> args = discussed on <a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page
</pre>
<pre class="literal-block">
@ -179,7 +190,7 @@
f_ID[N] = Nth column of local array calculated by a fix with ID
</pre>
<pre class="literal-block">
<em>custom</em> or <em>custom/mpiio</em> args = list of atom attributes
<em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em> args = list of atom attributes
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
@ -224,6 +235,7 @@ i_name = per-atom integer vector with name, managed by fix property/atom
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>dump myDump all atom 100 dump.atom
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
@ -274,6 +286,16 @@ multiple processors, each of which owns a subset of the atoms.</p>
default. For the <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, and <em>molfile</em> styles, sorting by
atom ID is on by default. See the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> doc
page for details.</p>
<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are identical
in command syntax to the corresponding styles without &#8220;gz&#8221;, however,
they generate compressed files using the zlib library. Thus the filename
suffix &#8221;.gz&#8221; is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed network
disallows using the fork() library call (which is needed for a pipe).
For the remainder of this doc page, you should thus consider the <em>atom</em>
and <em>atom/gz</em> styles (etc) to be inter-changeable, with the exception
of the required filename suffix.</p>
<p>As explained below, the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and
<em>xyz/mpiio</em> styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
@ -645,8 +667,13 @@ per-atom quantities which could then be output into dump files.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of the documentation.</p>
<p>To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package
- see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of
the documentation.</p>
<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are part
of the COMPRESS package. They are only enabled if LAMMPS was built
with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em> styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
@ -668,7 +695,8 @@ machines.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="dump_image.html"><em>dump image</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>,
<p><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
<a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>,
<a class="reference internal" href="undump.html"><em>undump</em></a></p>
</div>
<div class="section" id="default">

37
doc/dump.txt
View File

@ -7,6 +7,7 @@
:line
dump command :h3
"dump h5md"_dump_h5md.html command :h3
"dump image"_dump_image.html command :h3
"dump movie"_dump_image.html command :h3
"dump molfile"_dump_molfile.html command :h3
@ -17,19 +18,24 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {atom/mpiio} or {cfg} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/mpiio} :l
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} or {h5md} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/gz} or {custom/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
{atom} args = none
{atom/gz} args = none
{atom/mpiio} args = none
{cfg} args = same as {custom} args, see below
{cfg/gz} args = same as {custom} args, see below
{cfg/mpiio} args = same as {custom} args, see below
{dcd} args = none
{xtc} args = none
{xyz} args = none :pre
{xyz/gz} args = none :pre
{xyz/mpiio} args = none :pre
{h5md} args = discussed on "dump h5md"_dump_h5md.html doc page :pre
{image} args = discussed on "dump image"_dump_image.html doc page :pre
{movie} args = discussed on "dump image"_dump_image.html doc page :pre
@ -44,7 +50,7 @@ args = list of arguments for a particular style :l
f_ID = local vector calculated by a fix with ID
f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre
{custom} or {custom/mpiio} args = list of atom attributes
{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
@ -88,6 +94,7 @@ args = list of arguments for a particular style :l
dump myDump all atom 100 dump.atom
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
@ -136,6 +143,17 @@ default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
atom ID is on by default. See the "dump_modify"_dump_modify.html doc
page for details.
The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are identical
in command syntax to the corresponding styles without "gz", however,
they generate compressed files using the zlib library. Thus the filename
suffix ".gz" is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed network
disallows using the fork() library call (which is needed for a pipe).
For the remainder of this doc page, you should thus consider the {atom}
and {atom/gz} styles (etc) to be inter-changeable, with the exception
of the required filename suffix.
As explained below, the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and
{xyz/mpiio} styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
@ -569,9 +587,15 @@ per-atom quantities which could then be output into dump files.
[Restrictions:]
To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package
- see the "Making LAMMPS"_Section_start.html#start_2 section of
the documentation.
The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part
of the COMPRESS package. They are only enabled if LAMMPS was built
with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
are part of the MPIIO package. They are only enabled if LAMMPS was
@ -597,7 +621,8 @@ machines.
[Related commands:]
"dump image"_dump_image.html, "dump_modify"_dump_modify.html,
"dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
"dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html,
"undump"_undump.html
[Default:]

299
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@ -0,0 +1,299 @@
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<div class="section" id="dump-h5md-command">
<span id="index-0"></span><h1>dump h5md command<a class="headerlink" href="#dump-h5md-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>dump ID group-ID h5md N file.h5 args
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the dump</li>
<li>group-ID = ID of the group of atoms to be imaged</li>
<li>h5md = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a> doc page)</li>
<li>N = dump every this many timesteps</li>
<li>file.h5 = name of file to write to</li>
<li>args = list of data elements to dump, with their dump &#8220;subintervals&#8221;.
At least one element must be given and image may only be present if
position is specified first.</li>
</ul>
<pre class="literal-block">
position options
image
velocity options
force options
species options
file_from ID: do not open a new file, re-use the already opened file from dump ID
box value = <em>yes</em> or <em>no</em>
create_group value = <em>yes</em> or <em>no</em>
author value = quoted string
</pre>
<p>For the elements <em>position</em>, <em>velocity</em>, <em>force</em> and <em>species</em>, one
may specify a sub-interval to write the data only every N_element
iterations of the dump (i.e. every N*N_element time steps). This is
specified by the option</p>
<div class="highlight-python"><div class="highlight"><pre>every N_element
</pre></div>
</div>
<p>that follows directly the element declaration.</p>
</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>dump h5md1 all h5md 100 dump_h5md.h5 position image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
dump h5md1 all h5md 100 dump_h5md.h5 velocity author &quot;John Doe&quot;
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Dump a snapshot of atom coordinates every N timesteps in the
<a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> based <a class="reference external" href="http://nongnu.org/h5md/">H5MD</a> file format <a class="reference internal" href="#h5md-cpc"><span>(de Buyl)</span></a>.
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.</p>
<p>Several dumps may write to the same file, by using file_from and
referring to a previously defined dump. Several groups may also be
stored within the same file by defining several dumps. A dump that
refers (via <em>file_from</em>) to an already open dump ID and that concerns
another particle group must specify <em>create_group yes</em>.</p>
<p>Each data element is written every N*N_element steps. For <em>image</em>, no
subinterval is needed as it must be present at the same interval as
<em>position</em>. <em>image</em> must be given after <em>position</em> in any case. The
box information (edges in each dimension) is stored at the same
interval than the <em>position</em> element, if present. Else it is stored
every N steps.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.</p>
</div>
<p><strong>Use from write_dump:</strong></p>
<p>It is possible to use this dump style with the
<a class="reference internal" href="write_dump.html"><em>write_dump</em></a> command. In this case, the subintervals
must not be set at all. The write_dump command can be used either to
create a new file or to add current data to an existing dump file by
using the <em>file_from</em> keyword.</p>
<p>Typically, the <em>species</em> data is fixed. The following two commands
store the position data every 100 timesteps, with the image data, and
store once the species data in the same file.</p>
<div class="highlight-python"><div class="highlight"><pre>dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The number of atoms per snapshot cannot change with the h5md style.
The position data is stored wrapped (box boundaries not enforced, see
note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.</p>
<p>The <em>h5md</em> dump style is part of the USER-H5MD package. It is only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info. It also
requires (i) building the ch5md library provided with LAMMPS (See the
<a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.) and
(ii) having the <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> library installed (C bindings are
sufficient) on your system. The library ch5md is compiled with the
h5cc wrapper provided by the HDF5 library.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
<hr class="docutils" />
<p id="h5md-cpc"><strong>(de Buyl)</strong> de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data,
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
<a class="reference external" href="http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</a>.</p>
</div>
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124
doc/dump_h5md.txt Normal file
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@ -0,0 +1,124 @@
"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
dump h5md command :h3
[Syntax:]
dump ID group-ID h5md N file.h5 args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file.h5 = name of file to write to :l
args = list of data elements to dump, with their dump "subintervals".
At least one element must be given and image may only be present if
position is specified first. :l
position options
image
velocity options
force options
species options
file_from ID: do not open a new file, re-use the already opened file from dump ID
box value = {yes} or {no}
create_group value = {yes} or {no}
author value = quoted string :pre
For the elements {position}, {velocity}, {force} and {species}, one
may specify a sub-interval to write the data only every N_element
iterations of the dump (i.e. every N*N_element time steps). This is
specified by the option
every N_element :pre
that follows directly the element declaration.
:ule
[Examples:]
dump h5md1 all h5md 100 dump_h5md.h5 position image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre
[Description:]
Dump a snapshot of atom coordinates every N timesteps in the
"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.
Several dumps may write to the same file, by using file_from and
referring to a previously defined dump. Several groups may also be
stored within the same file by defining several dumps. A dump that
refers (via {file_from}) to an already open dump ID and that concerns
another particle group must specify {create_group yes}.
:link(h5md,http://nongnu.org/h5md/)
Each data element is written every N*N_element steps. For {image}, no
subinterval is needed as it must be present at the same interval as
{position}. {image} must be given after {position} in any case. The
box information (edges in each dimension) is stored at the same
interval than the {position} element, if present. Else it is stored
every N steps.
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
[Use from write_dump:]
It is possible to use this dump style with the
"write_dump"_write_dump.html command. In this case, the subintervals
must not be set at all. The write_dump command can be used either to
create a new file or to add current data to an existing dump file by
using the {file_from} keyword.
Typically, the {species} data is fixed. The following two commands
store the position data every 100 timesteps, with the image data, and
store once the species data in the same file.
dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species :pre
:line
[Restrictions:]
The number of atoms per snapshot cannot change with the h5md style.
The position data is stored wrapped (box boundaries not enforced, see
note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.
The {h5md} dump style is part of the USER-H5MD package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. It also
requires (i) building the ch5md library provided with LAMMPS (See the
"Making LAMMPS"_Section_start.html#start_3 section for more info.) and
(ii) having the "HDF5"_HDF5_ws library installed (C bindings are
sufficient) on your system. The library ch5md is compiled with the
h5cc wrapper provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
:line
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
:line
:link(h5md_cpc)
[(de Buyl)] de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data,
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
"\[arXiv:1308.6382\]"_http://arxiv.org/abs/1308.6382/.

8
doc/genindex.html
View File

@ -807,12 +807,12 @@
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<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>
@ -846,6 +846,10 @@
</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>

2
doc/package.html
View File

@ -173,6 +173,8 @@
Nthreads = # of GPU threads used per atom
<em>device</em> value = device_type
device_type = <em>kepler</em> or <em>fermi</em> or <em>cypress</em> or <em>generic</em>
<em>blocksize</em> value = size
size = thread block size for pair force computation
<em>intel</em> args = NPhi keyword value ...
Nphi = # of coprocessors per node
zero or more keyword/value pairs may be appended

2
doc/package.txt
View File

@ -51,6 +51,8 @@ args = arguments specific to the style :l
Nthreads = # of GPU threads used per atom
{device} value = device_type
device_type = {kepler} or {fermi} or {cypress} or {generic}
{blocksize} value = size
size = thread block size for pair force computation
{intel} args = NPhi keyword value ...
Nphi = # of coprocessors per node
zero or more keyword/value pairs may be appended

3
doc/pair_lj_cubic.html
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@ -127,6 +127,9 @@
<div class="section" id="pair-style-lj-cubic-command">
<span id="index-0"></span><h1>pair_style lj/cubic command<a class="headerlink" href="#pair-style-lj-cubic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cubic-gpu-command">
<h1>pair_style lj/cubic/gpu command<a class="headerlink" href="#pair-style-lj-cubic-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cubic-omp-command">
<h1>pair_style lj/cubic/omp command<a class="headerlink" href="#pair-style-lj-cubic-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">

1
doc/pair_lj_cubic.txt
View File

@ -7,6 +7,7 @@
:line
pair_style lj/cubic command :h3
pair_style lj/cubic/gpu command :h3
pair_style lj/cubic/omp command :h3
[Syntax:]

13
doc/pair_tersoff.html
View File

@ -133,6 +133,9 @@
<div class="section" id="pair-style-tersoff-cuda">
<h1>pair_style tersoff/cuda<a class="headerlink" href="#pair-style-tersoff-cuda" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-gpu">
<h1>pair_style tersoff/gpu<a class="headerlink" href="#pair-style-tersoff-gpu" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-kk">
<h1>pair_style tersoff/kk<a class="headerlink" href="#pair-style-tersoff-kk" title="Permalink to this headline"></a></h1>
</div>
@ -146,7 +149,7 @@
<div class="highlight-python"><div class="highlight"><pre>pair_style style
</pre></div>
</div>
<p>style = <em>tersoff</em> or <em>tersoff/table</em> or <em>tersoff/cuda</em> or <em>tersoff/omp</em> or <em>tersoff/table/omp</em></p>
<p>style = <em>tersoff</em> or <em>tersoff/table</em> or <em>tersoff/cuda</em> or <em>tersoff/gpu</em> or <em>tersoff/omp</em> or <em>tersoff/table/omp</em></p>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
@ -163,7 +166,7 @@ pair_coeff * * SiCGe.tersoff Si(D)
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>tersoff</em> style computes a 3-body Tersoff potential
<a class="reference internal" href="pair_tersoff_zbl.html#tersoff-1"><span>(Tersoff_1)</span></a> for the energy E of a system of atoms as</p>
<a class="reference internal" href="#tersoff-1"><span>(Tersoff_1)</span></a> for the energy E of a system of atoms as</p>
<img alt="_images/pair_tersoff_1.jpg" class="align-center" src="_images/pair_tersoff_1.jpg" />
<p>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
@ -256,15 +259,15 @@ be set to 0.0 if desired.</p>
<p>Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a> are not symmetric.</p>
Tersoff_2 <a class="reference internal" href="#tersoff-2"><span>(Tersoff_2)</span></a> are not symmetric.</p>
<p>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff potential. In particular, our form
reduces to the original Tersoff form when m = 3 and gamma = 1, while
it reduces to the form of <a class="reference internal" href="pair_tersoff_zbl.html#albe"><span>Albe et al.</span></a> when beta = 1 and m = 1.
it reduces to the form of <a class="reference internal" href="#albe"><span>Albe et al.</span></a> when beta = 1 and m = 1.
Note that in the current Tersoff implementation in LAMMPS, m must be
specified as either 3 or 1. Tersoff used a slightly different but
equivalent form for alloys, which we will refer to as Tersoff_2
potential <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a>. The <em>tersoff/table</em> style implements
potential <a class="reference internal" href="#tersoff-2"><span>(Tersoff_2)</span></a>. The <em>tersoff/table</em> style implements
Tersoff_2 parameterization only.</p>
<p>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma_ijk = omega_ik, lambda3 = 0 and the value of

3
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@ -9,6 +9,7 @@
pair_style tersoff command :h3
pair_style tersoff/table command :h3
pair_style tersoff/cuda :h3
pair_style tersoff/gpu :h3
pair_style tersoff/kk :h3
pair_style tersoff/omp :h3
pair_style tersoff/table/omp command :h3
@ -17,7 +18,7 @@ pair_style tersoff/table/omp command :h3
pair_style style :pre
style = {tersoff} or {tersoff/table} or {tersoff/cuda} or {tersoff/omp} or {tersoff/table/omp}
style = {tersoff} or {tersoff/table} or {tersoff/cuda} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp}
[Examples:]

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@ -127,6 +127,9 @@
<div class="section" id="pair-style-zbl-command">
<span id="index-0"></span><h1>pair_style zbl command<a class="headerlink" href="#pair-style-zbl-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-gpu-command">
<h1>pair_style zbl/gpu command<a class="headerlink" href="#pair-style-zbl-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-omp-command">
<h1>pair_style zbl/omp command<a class="headerlink" href="#pair-style-zbl-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">

1
doc/pair_zbl.txt
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@ -7,6 +7,7 @@
:line
pair_style zbl command :h3
pair_style zbl/gpu command :h3
pair_style zbl/omp command :h3
[Syntax:]

2
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