diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html new file mode 100644 index 0000000000000000000000000000000000000000..d01062f47364d86df20dbf295747014dcb412797 --- /dev/null +++ b/doc/doc2/Manual.html.html @@ -0,0 +1,318 @@ +<HTML> +<HTML> +<!-- HTML_ONLY --> +<HEAD> +<TITLE>LAMMPS Users Manual</TITLE> +<META NAME="docnumber" CONTENT="28 Jul 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>28 Jul 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>