diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index b276794a5..441e9cc8f 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,340 +1,340 @@
LAMMPS Users Manual
-
+
"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
LAMMPS Documentation :c,h3
-22 Sep 2016 version :c,h4
+21 Sep 2016 version :c,h4
Version info: :h4
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on "this page of
the WWW site"_bug. Every 2-4 months one of the incremental releases
is subjected to more thorough testing and labeled as a {stable} version.
Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :l
:ule
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 current core group of LAMMPS developers is at Sandia National
Labs and Temple University:
"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
Aidan Thompson, athomps at sandia.gov :l
Stan Moore, stamoore at sandia.gov :l
"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
:ule
Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
all at Sandia. The [LAMMPS home page] at
"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information
about the code and its uses. Interaction with external LAMMPS developers,
bug reports and feature requests are mainly coordinated through the
"LAMMPS project on GitHub."_https://github.com/lammps/lammps
The lammps.org domain, currently hosting "public continuous integration
testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
RPM and Windows installer packages"_http://rpm.lammps.org is located
at Temple University and managed by Richard Berger,
richard.berger at temple.edu.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
:link(ako,http://goo.gl/1wk0)
: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
"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 "GPU package"_accelerate_gpu.html :ulb,b
5.3.2 "USER-INTEL package"_accelerate_intel.html :b
5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
5.3.4 "USER-OMP package"_accelerate_omp.html :b
5.3.5 "OPT package"_accelerate_opt.html :ule,b
5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
6.3 "CHARMM and AMBER force fields"_howto_3 :b
6.4 "Running multiple simulations from one input script"_howto_4 :b
6.5 "Multi-replica simulations"_howto_5 :b
6.6 "Granular models"_howto_6 :b
6.7 "TIP3P water model"_howto_7 :b
6.8 "TIP4P water model"_howto_8 :b
6.9 "SPC water model"_howto_9 :b
6.10 "Coupling LAMMPS to other codes"_howto_10 :b
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b
6.18 "Elastic constants"_howto_18 :b
6.19 "Library interface to LAMMPS"_howto_19 :b
6.20 "Calculating thermal conductivity"_howto_20 :b
6.21 "Calculating viscosity"_howto_21 :b
6.22 "Calculating a diffusion coefficient"_howto_22 :b
6.23 "Using chunks to calculate system properties"_howto_23 :b
6.24 "Setting parameters for pppm/disp"_howto_24 :b
6.25 "Polarizable models"_howto_25 :b
6.26 "Adiabatic core/shell model"_howto_26 :b
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
10.3 "Compute styles"_mod_3 :b
10.4 "Dump styles"_mod_4 :b
10.5 "Dump custom output options"_mod_5 :b
10.6 "Fix styles"_mod_6 :b
10.7 "Input script commands"_mod_7 :b
10.8 "Kspace computations"_mod_8 :b
10.9 "Minimization styles"_mod_9 :b
10.10 "Pairwise potentials"_mod_10 :b
10.11 "Region styles"_mod_11 :b
10.12 "Body styles"_mod_12 :b
10.13 "Thermodynamic output options"_mod_13 :b
10.14 "Variable options"_mod_14 :b
10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
"Python interface"_Section_python.html :l
11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b
11.2 "Overview of using Python from a LAMMPS script"_py_2 :b
11.3 "Building LAMMPS as a shared library"_py_3 :b
11.4 "Installing the Python wrapper into Python"_py_4 :b
11.5 "Extending Python with MPI to run in parallel"_py_5 :b
11.6 "Testing the Python-LAMMPS interface"_py_6 :b
11.7 "Using LAMMPS from Python"_py_7 :b
11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b
"Errors"_Section_errors.html :l
12.1 "Common problems"_err_1 :ulb,b
12.2 "Reporting bugs"_err_2 :b
12.3 "Error & warning messages"_err_3 :ule,b
"Future and history"_Section_history.html :l
13.1 "Coming attractions"_hist_1 :ulb,b
13.2 "Past versions"_hist_2 :ule,b
:ole
:link(intro_1,Section_intro.html#intro_1)
:link(intro_2,Section_intro.html#intro_2)
:link(intro_3,Section_intro.html#intro_3)
:link(intro_4,Section_intro.html#intro_4)
:link(intro_5,Section_intro.html#intro_5)
:link(start_1,Section_start.html#start_1)
:link(start_2,Section_start.html#start_2)
:link(start_3,Section_start.html#start_3)
:link(start_4,Section_start.html#start_4)
:link(start_5,Section_start.html#start_5)
:link(start_6,Section_start.html#start_6)
:link(start_7,Section_start.html#start_7)
:link(start_8,Section_start.html#start_8)
:link(start_9,Section_start.html#start_9)
:link(cmd_1,Section_commands.html#cmd_1)
:link(cmd_2,Section_commands.html#cmd_2)
:link(cmd_3,Section_commands.html#cmd_3)
:link(cmd_4,Section_commands.html#cmd_4)
:link(cmd_5,Section_commands.html#cmd_5)
:link(pkg_1,Section_packages.html#pkg_1)
:link(pkg_2,Section_packages.html#pkg_2)
:link(acc_1,Section_accelerate.html#acc_1)
:link(acc_2,Section_accelerate.html#acc_2)
:link(acc_3,Section_accelerate.html#acc_3)
:link(acc_4,Section_accelerate.html#acc_4)
:link(howto_1,Section_howto.html#howto_1)
:link(howto_2,Section_howto.html#howto_2)
:link(howto_3,Section_howto.html#howto_3)
:link(howto_4,Section_howto.html#howto_4)
:link(howto_5,Section_howto.html#howto_5)
:link(howto_6,Section_howto.html#howto_6)
:link(howto_7,Section_howto.html#howto_7)
:link(howto_8,Section_howto.html#howto_8)
:link(howto_9,Section_howto.html#howto_9)
:link(howto_10,Section_howto.html#howto_10)
:link(howto_11,Section_howto.html#howto_11)
:link(howto_12,Section_howto.html#howto_12)
:link(howto_13,Section_howto.html#howto_13)
:link(howto_14,Section_howto.html#howto_14)
:link(howto_15,Section_howto.html#howto_15)
:link(howto_16,Section_howto.html#howto_16)
:link(howto_17,Section_howto.html#howto_17)
:link(howto_18,Section_howto.html#howto_18)
:link(howto_19,Section_howto.html#howto_19)
:link(howto_20,Section_howto.html#howto_20)
:link(howto_21,Section_howto.html#howto_21)
:link(howto_22,Section_howto.html#howto_22)
:link(howto_23,Section_howto.html#howto_23)
:link(howto_24,Section_howto.html#howto_24)
:link(howto_25,Section_howto.html#howto_25)
:link(howto_26,Section_howto.html#howto_26)
:link(howto_27,Section_howto.html#howto_27)
:link(mod_1,Section_modify.html#mod_1)
:link(mod_2,Section_modify.html#mod_2)
:link(mod_3,Section_modify.html#mod_3)
:link(mod_4,Section_modify.html#mod_4)
:link(mod_5,Section_modify.html#mod_5)
:link(mod_6,Section_modify.html#mod_6)
:link(mod_7,Section_modify.html#mod_7)
:link(mod_8,Section_modify.html#mod_8)
:link(mod_9,Section_modify.html#mod_9)
:link(mod_10,Section_modify.html#mod_10)
:link(mod_11,Section_modify.html#mod_11)
:link(mod_12,Section_modify.html#mod_12)
:link(mod_13,Section_modify.html#mod_13)
:link(mod_14,Section_modify.html#mod_14)
:link(mod_15,Section_modify.html#mod_15)
:link(py_1,Section_python.html#py_1)
:link(py_2,Section_python.html#py_2)
:link(py_3,Section_python.html#py_3)
:link(py_4,Section_python.html#py_4)
:link(py_5,Section_python.html#py_5)
:link(py_6,Section_python.html#py_6)
:link(err_1,Section_errors.html#err_1)
:link(err_2,Section_errors.html#err_2)
:link(err_3,Section_errors.html#err_3)
:link(hist_1,Section_history.html#hist_1)
:link(hist_2,Section_history.html#hist_2)