patch 22Aug18

Doc updates for release

README

@@ -36,7 +36,14 @@ tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-doc/Manual.html	           the LAMMPS manual
-doc/Section_intro.html	   hi-level introduction to LAMMPS
-doc/Section_start.html	   how to build and use LAMMPS
-doc/Developer.pdf          LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html                # creates HTML pages in doc/html
+% make pdf                 # creates Manual.pdf and Developer.pdf

cmake/CMakeLists.txt

@@ -377,6 +377,9 @@ endif()
 if(PKG_LATTE)
   option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
   if(DOWNLOAD_LATTE)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
     message(STATUS "LATTE not found - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
@@ -479,6 +482,9 @@ if(PKG_MSCG)
   find_package(GSL REQUIRED)
   option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
   if(DOWNLOAD_MSCG)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
     include(ExternalProject)
     if(NOT LAPACK_FOUND)
       set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
@@ -731,6 +737,11 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+  if(PKG_KSPACE)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+  endif()
+
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
 
   # detects styles which have KOKKOS version

cmake/README.md

@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BUILD_EXE</code></td>
+  <td>control whether to build LAMMPS executable</td>
+  <td>
+  <dl>
+    <dt><code>on</code> (default)</dt>
+    <dt><code>off</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BUILD_SHARED_LIBS</code></td>
   <td>control whether to build LAMMPS as a shared-library</td>

doc/src/Build.txt

@@ -1,5 +1,5 @@
 "Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run.html :c
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
@@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
    Build_settings
    Build_package
    Build_extras
+   Build_windows
 
 END_RST -->
 
@@ -39,7 +40,8 @@ END_RST -->
 "Basic build options"_Build_basics.html
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html :all(b)
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

doc/src/Build_cmake.txt

@@ -13,12 +13,10 @@ This page is a short summary of how to use CMake to build LAMMPS.
 Details on CMake variables that enable specific LAMMPS build options
 are given on the pages linked to from the "Build"_Build.html doc page.
 
-Richard Berger (Temple U) has also written a more comprehensive guide
+Richard Berger (Temple U) has also written a "more comprehensive
+guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
 for how to use CMake to build LAMMPS.  If you are new to CMake it is a
-good place to start:
-
-"Bulding LAMMPS using
-CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+good place to start.
 
 :line
 
@@ -81,8 +79,9 @@ directory to un-install all packages.  The purge removes all the *.h
 files auto-generated by make.
 
 You must have CMake version 2.8 or later on your system to build
-LAMMPS.  If you include the GPU or KOKKOS packages, CMake version 3.2
-or later is required.  Installation instructions for CMake are below.
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
 
 After the initial build, if you edit LAMMPS source files, or add your
 own new files to the source directory, you can just re-type make from

doc/src/Build_extras.txt

@@ -48,7 +48,7 @@ This is the list of packages that may require additional steps.
 "USER-QMMM"_#user-qmmm,
 "USER-QUIP"_#user-quip,
 "USER-SMD"_#user-smd,
-"USER-VTK"_#user-vtk :tb(c=6,ea=c)
+"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
 
 :line
 
@@ -175,8 +175,15 @@ package?" page.
 [CMake build]:
 
 -D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # path to KIM shared library (only needed if a custom location) 
--D KIM_INCLUDE_DIR=path  # path to KIM include directory (only needed if a custom location) :pre
+-D KIM_LIBRARY=path      # KIM library file (only needed if a custom location) 
+-D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
+inside the CMake build directory.  If the KIM library is already on
+your system (in a location CMake cannot find it), KIM_LIBRARY is the
+filename (plus path) of the KIM library file, not the directory the
+library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
+file is in.
 
 [Traditional make]:
 
@@ -296,7 +303,13 @@ library.
 [CMake build]:
 
 -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
--D LATTE_LIBRARY=path      # path to LATTE shared library (only needed if a custom location) :pre
+-D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location) :pre
+
+If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and
+built inside the CMake build directory.  If the LATTE library is
+already on your system (in a location CMake cannot find it),
+LATTE_LIBRARY is the filename (plus path) of the LATTE library file,
+not the directory the library file is in.
 
 [Traditional make]:
 
@@ -371,8 +384,15 @@ lib/mscg/README and MSCG/Install files for more details.
 [CMake build]:
 
 -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
--D MSCG_LIBRARY=path      # path to MSCG shared library (only needed if a custom location) 
--D MSCG_INCLUDE_DIR=path  # path to MSCG include directory (only needed if a custom location) :pre
+-D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location) 
+-D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
+inside the CMake build directory.  If the MSCG library is already on
+your system (in a location CMake cannot find it), MSCG_LIBRARY is the
+filename (plus path) of the MSCG library file, not the directory the
+library file is in.  MSCG_INCLUDE_DIR is the directory the MSCG
+include file is in.
 
 [Traditional make]:
 
@@ -515,8 +535,15 @@ library"_voro_home.
 [CMake build]:
 
 -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
--D VORO_LIBRARY=path      # (only needed if at custom location) path to VORO shared library
--D VORO_INCLUDE_DIR=path  # (only needed if at custom location) path to VORO include directory :pre
+-D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location) 
+-D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
+built inside the CMake build directory.  If the Voro++ library is
+already on your system (in a location CMake cannot find it),
+VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in.  VORO_INCLUDE_DIR is the
+directory the Voro++ include file is in.
 
 [Traditional make]:
 
@@ -877,7 +904,10 @@ Eigen3 is a template library, so you do not need to build it.
 -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
 -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location) :pre
 
-Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library.
+If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
+inside the CMake build directory.  If the Eig3n3 library is already on
+your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
+is the directory the Eigen3++ include file is in.
 
 [Traditional make]:
 

doc/src/Build_package.txt

@@ -59,7 +59,7 @@ packages:
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,
 "USER-SMD"_Build_extras.html#user-smd,
-"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c)
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
 
 The mechanism for including packages is simple but different for CMake
 versus make.

doc/src/Build_windows.txt

@@ -0,0 +1,97 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.  
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or 
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested. 
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers.  We instead rely on the feedback of the users
+of these precompiled LAMMPS packages for Windows.  We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.

doc/src/Commands.txt

@@ -1,4 +1,4 @@
-"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
 "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
 Section"_Packages.html :c
 

doc/src/Howto.txt

@@ -8,27 +8,44 @@ Section"_Examples.html :c
 
 :line
 
-How to discussions :h2
+Howto discussions :h2
 
 These doc pages describe how to perform various tasks with LAMMPS,
 both for users and developers.  The
 "glossary"_http://lammps.sandia.gov website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.
-
-The example input scripts included in the examples dir of the LAMMPS
+terminology with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the examples dir of the LAMMPS
 distribution and highlighted on the "Examples"_Examples.html doc page
 also show how to setup and run various kinds of simulations.
 
+Tutorials howto :h3
+
 <!-- RST
 
 .. toctree::
+   :name: tutorials
    :maxdepth: 1
 
    Howto_github
    Howto_pylammps
    Howto_bash
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+General howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: general
    :maxdepth: 1
 
    Howto_restart
@@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
    Howto_library
    Howto_couple
 
-.. toctree::
-   :maxdepth: 1
+END_RST -->
 
-   Howto_output
-   Howto_chunk
+<!-- HTML_ONLY -->
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"Run multiple simulations from one input script"_Howto_multiple.html
+"Multi-replica simulations"_Howto_replica.html
+"Library interface to LAMMPS"_Howto_library.html
+"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Settings howto :h3
+
+<!-- RST
 
 .. toctree::
+   :name: settings
    :maxdepth: 1
 
    Howto_2d
    Howto_triclinic
-   Howto_walls
-   Howto_nemd
-   Howto_granular
-   Howto_spherical
-   Howto_dispersion
-
-.. toctree::
-   :maxdepth: 1
-
-   Howto_temperature
    Howto_thermostat
    Howto_barostat
+   Howto_walls
+   Howto_nemd
+   Howto_dispersion
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+
+Analysis howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: analysis
+   :maxdepth: 1
+
+   Howto_output
+   Howto_chunk
+   Howto_temperature
    Howto_elastic
    Howto_kappa
    Howto_viscosity
    Howto_diffusion
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+"Calculate temperature"_Howto_temperature.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Force fields howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: force
    :maxdepth: 1
 
    Howto_bioFF
@@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
    Howto_tip4p
    Howto_spc
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Packages howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: packages
    :maxdepth: 1
 
+   Howto_spherical
+   Howto_granular
    Howto_body
    Howto_polarizable
    Howto_coreshell
@@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
 
 END_RST -->
 
+
 <!-- HTML_ONLY -->
 
-"Using GitHub with LAMMPS"_Howto_github.html
-"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
-
-"Restart a simulation"_Howto_restart.html
-"Visualize LAMMPS snapshots"_Howto_viz.html
-"Run multiple simulations from one input script"_Howto_multiple.html
-"Multi-replica simulations"_Howto_replica.html
-"Library interface to LAMMPS"_Howto_library.html
-"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
-
-"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
-"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
-
-"2d simulations"_Howto_2d.html
-"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
-"Walls"_Howto_walls.html
-"NEMD simulations"_Howto_nemd.html
-"Granular models"_Howto_granular.html
 "Finite-size spherical and aspherical particles"_Howto_spherical.html
-"Long-range dispersion settings"_Howto_dispersion.html :all(b)
-
-"Calculate temperature"_Howto_temperature.html
-"Thermostats"_Howto_thermostat.html
-"Barostats"_Howto_barostat.html
-"Calculate elastic constants"_Howto_elastic.html
-"Calculate thermal conductivity"_Howto_kappa.html
-"Calculate viscosity"_Howto_viscosity.html
-"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
-
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
-"TIP3P water model"_Howto_tip3p.html
-"TIP4P water model"_Howto_tip4p.html
-"SPC water model"_Howto_spc.html :all(b)
-
+"Granular models"_Howto_granular.html
 "Body style particles"_Howto_body.html
 "Polarizable models"_Howto_polarizable.html
 "Adiabatic core/shell model"_Howto_coreshell.html

doc/src/Howto_diffusion.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Calculate a diffusion coefficient :h3
+Calculate diffusion coefficients :h3
 
 The diffusion coefficient D of a material can be measured in at least
 2 ways using various options in LAMMPS.  See the examples/DIFFUSE

doc/src/Howto_dispersion.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Long-raage dispersion settings :h3
+Long-range dispersion settings :h3
 
 The PPPM method computes interactions by splitting the pair potential
 into two parts, one of which is computed in a normal pairwise fashion,

doc/src/Howto_temperature.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Calcalate temperature :h3
+Calculate temperature :h3
 
 Temperature is computed as kinetic energy divided by some number of
 degrees of freedom (and the Boltzmann constant).  Since kinetic energy

doc/src/Intro_authors.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-LAMMPS authors :h3
+Authors of LAMMPS :h3
 
 The primary LAMMPS developers are at Sandia National Labs and Temple
 University:
@@ -15,7 +15,8 @@ University:
 "Steve Plimpton"_sjp, sjplimp at sandia.gov
 Aidan Thompson, athomps at sandia.gov
 Stan Moore, stamoor at sandia.gov
-Axel Kohlmeyer, akohlmey at gmail.com :ul
+Axel Kohlmeyer, akohlmey at gmail.com
+Richard Berger, richard.berger at temple.edu :ul
 
 :link(sjp,http://www.cs.sandia.gov/~sjplimp)
 
@@ -24,26 +25,31 @@ and Ray Shan, now at Materials Design.
 
 :line
 
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort.  Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
+The "Authors page"_http://lammps.sandia.gov/authors.html of the
+"LAMMPS website"_lws has a comprehensive list of all the individuals
+who have contributed code for a new feature or command or tool to
+LAMMPS.
 
-Richard Berger (Temple U), Python interface, GitHub site, Sphinx doc pages
+:line
+
+The following folks deserve special recognition.  Many of the packages
+they have written are unique for an MD code and LAMMPS would not be as
+general-purpose as it is without their expertise and efforts.
+
+Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF
+Mike Brown (Intel), GPU and USER-INTEL packages
+Colin Denniston (U Western Ontario), USER-LB package
+Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages
+Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
+Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
+Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
+Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
+Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
+Mike Parks (Sandia), PERI package for Peridynamics
 Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
-Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
+Christian Trott (Sandia), USER-CUDA and KOKKOS packages
+Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
+Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
 
 :line
 
@@ -58,322 +64,3 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
 Steve Lustig (Dupont)
 Jim Belak and Roy Pollock (LLNL) :ul
 
-:line
-
-Here is a timeline for when various individuals contributed to a new
-feature or command or tool added to LAMMPS:
-
-Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U)
-Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
-Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
-Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
-May18 : fix bond/react : Jake Gissinger (CU Boulder)
-Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
-Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U) 
-Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
-Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
-Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
-Dec17 : fix python/move : Richard Berger (Temple U)
-Nov17 : pair extep : Jaap Kroes (Radboud U)
-Oct17 : USER-UEF package : David Nicholson (MIT)
-Oct17 : fix rhok : Ulf Pederson (Roskilde U)
-Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
-Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
-Sep17 : fix latte : Christian Negre (LANL)
-Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
-Aug17 : USER-MESO package : Zhen Li (Brown University)
-Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
-Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
-Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
-Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
-Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
-Jun17 : compute cnp/atom : Paulo Branicio (USC)
-May17 : fix python and pair python : Richard Berger (Temple U)
-May17 : pair edip/multi : Chao Jiang (U Wisconsin)
-May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
-Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
-Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
-Mar17 : fix filter/corotate : Lukas Fath (KIT)
-Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
-Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
-Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
-Jan17 : fix mscg : Lauren Abbott (Sandia)
-Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
-Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
-Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
-Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
-Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
-Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
-Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
-Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
-Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
-Sep16 : kspace pppm/kk : Stan Moore (Sandia)
-Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
-Aug16 : fix controller : Aidan Thompson (Sandia)
-Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
-Jul16 : dihedral spherical : Andrew Jewett
-Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
-Jun16 : fix orient/bcc : Tegar Wicaksono (UBC) 
-Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
-Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
-May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
-Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
-Apr16 : bond write : Axel Kohlmeyer (Temple U)
-Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
-Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
-Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
-Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
-Dec15 : fix qeq/fire : Ray Shan (Sandia)
-Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
-Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
-Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
-Oct15 : displace_atoms variable option : Reese Jones (Sandia)
-Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
-Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
-Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
-Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
-Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
-Aug15 : timer command : Axel Kohlmeyer (Temple U)
-Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
-Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
-Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
-Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
-Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
-Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
-Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
-Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
-Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
-Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
-Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
-Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
-Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
-Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
-Feb15 : fix tfmc : Kristof Bal (U of Antwerp) 
-Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
-Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
-Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
-Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
-Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF) 
-Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
-Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
-Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
-Aug14 : USER-INTEL package : Mike Brown (Intel)
-May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
-May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
-Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
-Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
-Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
-Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
-Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
-Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
-Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
-Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
-Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
-Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
-Sep13 : xmgrace tool : Vikas Varshney
-Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
-Aug13 : pair nm and variants : Julien Devemy (ICCF)
-Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
-Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
-Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
-Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
-Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
-Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia) 
-Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
-Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
-Jun13 : fix tune/kspace : Paul Crozier (Sandia)
-Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
-May13 : compute msd/nongauss : Rob Hoy
-May13 : pair list : Axel Kohlmeyer (Temple U)
-May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
-Apr13 : dump_modify nfile and fileper : Christopher Knight
-Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
-Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
-Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
-Feb13 : fix species : Ray Shan (Sandia)
-Jan13 : compute voronoi/atom : Daniel Schwen
-Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
-Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
-Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
-Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
-Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
-Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
-Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
-Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
-Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
-Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
-Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
-Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
-Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
-Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
-Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
-May12 : read_dump : Tim Sirk (ARL)
-May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
-May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
-Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
-Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
-Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
-Feb12 : pair_style beck : Jon Zimmerman (Sandia)
-Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
-Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
-Jan12 : dihedral_style table : Andrew Jewett (UCSB)
-Jan12 : angle_style dipole : Mario Orsi
-Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
-Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
-Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
-Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
-Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
-Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
-Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
-Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
-Sep11 : pair_style edip : Luca Ferraro (CASPUR)
-Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
-Aug11 : fix restrain : Craig Tenney (Sandia)
-Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
-Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
-Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
-Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
-Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
-Aug11 : pair_style dipole/sf : Mario Orsi
-Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
-Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \
-  Axel Kohlmeyer (Temple U)
-Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
-  Chandra Veer Singh (Cornell)
-Jun11 : Windows build option via Microsoft Visual Studio : \
-  Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : dump image : Nathan Fabian (Sandia)
-May11 : pppm GPU single and double : Mike Brown (ORNL)
-May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
-2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
-- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
-- : fix adapt and compute ti for thermodynamic integration for \
-  free energies : Sai Jayaraman (Sandia)
-- : pair_style born and gauss : Sai Jayaraman (Sandia)
-- : stochastic rotation dynamics (SRD) via fix srd : \
-  Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
-- : ipp Perl script tool : Reese Jones (Sandia)
-- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
-- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
-- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
-- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
-- : fix ave/correlate :  Benoit Leblanc, Dave Rigby, \
-  Paul Saxe (Materials Design) and Reese Jones (Sandia)
-- : pair_style peri/lps : Mike Parks (Sandia)
-- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
-- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U) 
-- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
-- : public SVN & Git repositories for LAMMPS : \
-  Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
-- : compute heat/flux : German Samolyuk (ORNL) and \
-  Mario Pinto (Computational Research Lab, Pune, India)
-- : pair_style yukawa/colloid : Randy Schunk (Sandia)
-- : fix wall/colloid : Jeremy Lechman (Sandia)
-2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
-- : concentration-dependent EAM potential : \
-  Alexander Stukowski (Technical University of Darmstadt)
-- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
-- : min_style hftn : Todd Plantenga (Sandia)
-- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
-- : dump cfg : Liang Wan (Chinese Academy of Sciences)
-- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
-- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
-- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
-- : fix langevin tally : Carolyn Phillips (U Michigan)
-- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
-  Philip Howell (Siemens), Vikas Varsney (AFRL)
-- : region cone : Pim Schravendijk
-- : pair_style born/coul/long : Ahmed Ismail (Sandia)
-- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
-- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
-- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
-- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
-2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
-- : peridynamics : Mike Parks (Sandia)
-- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
-- : GROMACS pair potentials : Mark Stevens (Sandia)
-- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
-- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
-- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
-- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
-- : pair_style lubricate : Randy Schunk (Sandia)
-- : compute ackland/atom : Gerolf Ziegenhain
-- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
-  Pieter in 't Veld (Sandia)
-- : AI-REBO bond-order potential : Ase Henry (MIT)
-- : making LAMMPS a true "object" that can be instantiated \
-  multiple times, e.g. as a library : Ben FrantzDale (RPI)
-- : pymol_asphere viz tool : Mike Brown (Sandia)
-2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
-- : tensile and shear deformations : Pieter in 't Veld (Sandia)
-- : GayBerne potential : Mike Brown (Sandia)
-- : ellipsoidal particles : Mike Brown (Sandia)
-- : colloid potentials : Pieter in 't Veld (Sandia)
-- : fix heat : Paul Crozier and Ed Webb (Sandia)
-- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
-- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
-- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
-- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
-- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
-- : MEAM potential : Greg Wagner (Sandia)
-- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
-  James Fischer (High Performance Technologies), \
-  David Richie and Vincent Natoli (Stone Ridge Technologies)
-2006 : fix wall/lj126 : Mark Stevens (Sandia)
-- : Stillinger-Weber and Tersoff potentials : \
-  Aidan Thompson and Xiaowang Zhou (Sandia)
-- : region prism : Pieter in 't Veld (Sandia)
-- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : OPLS dihedral potential: Mark Stevens (Sandia)
-- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
-- : faster pair hybrid potential: James Fischer \
-    (High Performance Technologies, Inc), Vincent Natoli and \
-    David Richie (Stone Ridge Technology)
-- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
-- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
-- : grain boundary orientation fix : Koenraad Janssens and \
-  David Olmsted (Sandia)
-- : pair_style lj/smooth potential : Craig Maloney (UCSB) 
-- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
-  (Johns Hopkins U) and Paul Crozier (Sandia)
-- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
-- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
-    Mark Stevens (Sandia)
-- : Finnis/Sinclair EAM: Tim Lau (MIT)
-- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
-    Frank van Swol (Sandia)
-- : TIP4P potential (4-site water): Ahmed Ismail and \
-  Amalie Frischknecht (Sandia)
-2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
-- : compressed dump files: Erik Luijten (U Illinois)
-- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
-- : electric field fix: Christina Payne (Vanderbilt U)
-- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
-  Vikas Varshney (U Akron)
-- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
-- : Morse bond potential: Jeff Greathouse (Sandia)
-- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
-- : force tables for long-range Coulombics: Paul Crozier (Sandia)
-2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
-  Christian Burisch (Bochum University, Germany)
-- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
-- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
-    Andrey Kalinichev (Sandia)
-- : parallel tempering: Mark Sears (Sandia)
-earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
-- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
-- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
-- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
-- : HTFN energy minimizer: Todd Plantenga (Sandia)
-- : class 2 force fields: Eric Simon (Cray)
-- : NVT/NPT integrators: Mark Stevens (Sandia)
-- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
-- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Aug 2018 version">
+<META NAME="docnumber" CONTENT="22 Aug 2018 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>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-16 Aug 2018 version :c,h2
+22 Aug 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 
@@ -66,7 +66,7 @@ every LAMMPS command.
 
 .. toctree::
    :maxdepth: 2
-   :numbered:
+   :numbered: 3
    :caption: User Documentation
    :name: userdoc
    :includehidden:
@@ -74,7 +74,7 @@ every LAMMPS command.
    Intro
    Install
    Build
-   Run
+   Run_head
    Commands
    Packages
    Speed
@@ -112,7 +112,7 @@ END_RST -->
 "Introduction"_Intro.html :olb,l
 "Install LAMMPS"_Install.html :l
 "Build LAMMPS"_Build.html :l
-"Run LAMMPS"_Run.html :l
+"Run LAMMPS"_Run_head.html :l
 "Commands"_Commands.html :l
 "Optional packages"_Packages.html :l
 "Accelerate performance"_Speed.html :l

doc/src/Manual_build.txt

@@ -81,7 +81,7 @@ sudo yum install python3-virtualenv :pre
 
 Fedora (since version 22) :h4
 
-sudo dnf install python3-virtualenv pre
+sudo dnf install python3-virtualenv :pre
 
 MacOS X :h4
 

doc/src/Packages_details.txt

@@ -382,6 +382,11 @@ switches"_Run_options.html.  Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
 have styles optimized for CPUs, KNLs, and GPUs.
 
 You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
 
 [Authors:] The KOKKOS package was created primarily by Christian Trott
 and Stan Moore (Sandia), with contributions from other folks as well.

doc/src/Packages_standard.txt

@@ -25,42 +25,42 @@ refers to the examples/USER/atc directory.  The "Library" column
 indicates whether an extra library is needed to build and use the
 package:
 
-dash = no library
+no  = no library
 sys = system library: you likely have it on your machine
 int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
-"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
-"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
-"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
-"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no
+"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no
+"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no
+"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no
+"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys
+"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no
+"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no
 "GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no
 "KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no
 "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
+"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
 "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, -
-"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
-"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, n/a, no, no
+"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
+"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
 "MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
 "REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
-"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
-"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
+"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
+"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
+"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
+"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no
+"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no
+"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no
+"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l)

doc/src/Packages_user.txt

@@ -32,7 +32,7 @@ refers to the examples/USER/atc directory.  The "Library" column
 indicates whether an extra library is needed to build and use the
 package:
 
-dash = no library
+no  = no library
 sys = system library: you likely have it on your machine
 int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
@@ -40,35 +40,35 @@ ext = external library: you will need to download and install it on your machine
 Package, Description, Doc page, Example, Library
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
+"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
+"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
 "USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
-"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no
+"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no
+"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no
+"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no
+"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no
+"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext
+"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
+"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
+"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
+"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
+"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
+"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
+"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
-"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
+"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
-"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
+"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
+"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
+"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)

doc/src/Run_basics.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)

doc/src/Run_options.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)

doc/src/Run_output.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)

doc/src/Run_windows.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)

doc/src/Speed_compare.txt

@@ -9,65 +9,108 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Comparison of various accelerator packages :h3
 
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
 The next section compares and contrasts the various accelerator
 options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
+run on GPUs, optimize for vector units on CPUs and run on Intel
+Xeon Phi (co-)processors.
 
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
+All of these packages can accelerate a LAMMPS calculation taking
+advantage of hardware features, but they do it in different ways
+and acceleration is not always guaranteed.
 
 As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other.  We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine.  See the benchmarking
+one package may be faster than the other.  We give some guidelines
+below, but the best way to determine which package is faster for your
+input script is to try multiple of them on your machine and experiment
+with available performance tuning settings.  See the benchmarking
 section below for examples where this has been done.
 
 [Guidelines for using each package optimally:]
 
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
+Both, the GPU and the KOKKOS package allows you to assign multiple
+MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
+can lead to a speedup through better utilization of the GPU (by
+overlapping computation and data transfer) and more efficient
+computation of the non-GPU accelerated parts of LAMMPS through MPI
+parallelization, as all system data is maintained and updated on
+the host. For KOKKOS, there is less to no benefit from this, due
+to its different memory management model, which tries to retain
+data on the GPU.
+ :ulb,l
 
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep.  The
-KOKKOS/CUDA package only does this on timesteps when a CPU calculation
-is required (e.g. to invoke a fix or compute that is non-GPU-ized).
-Hence, if you can formulate your input script to only use GPU-ized
-fixes and computes, and avoid doing I/O too often (thermo output, dump
-file snapshots, restart files), then the data transfer cost of the
-KOKKOS/CUDA package can be very low, causing it to run faster than the
-GPU package. :l
+The GPU package moves per-atom data (coordinates, forces, and
+(optionally) neighbor list data, if not computed on the GPU) between
+the CPU and GPU at every timestep.  The KOKKOS/CUDA package only does
+this on timesteps when a CPU calculation is required (e.g. to invoke
+a fix or compute that is non-GPU-ized). Hence, if you can formulate
+your input script to only use GPU-ized fixes and computes, and avoid
+doing I/O too often (thermo output, dump file snapshots, restart files),
+then the data transfer cost of the KOKKOS/CUDA package can be very low,
+causing it to run faster than the GPU package. :l
 
-The GPU package is often faster than the KOKKOS/CUDA package, if the
-number of atoms per GPU is smaller.  The crossover point, in terms of
-atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
-strongly on the pair style.  For example, for a simple Lennard Jones
+The GPU package is often faster than the KOKKOS/CUDA package, when the
+number of atoms per GPU is on the smaller side.  The crossover point,
+in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
+depends strongly on the pair style.  For example, for a simple Lennard Jones
 system the crossover (in single precision) is often about 50K-100K
 atoms per GPU.  When performing double precision calculations the
 crossover point can be significantly smaller. :l
 
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU.  If the GPU package is running with several MPI processes
+Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
+etc) on the CPU.  If the GPU package is running with several MPI processes
 assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
+spread across more CPUs and hence the GPU package can run faster in these
+cases. :l
 
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU.  Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU.  In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l
+When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
+performance depends to some extent on the available bandwidth between
+the CPUs and the GPU. This can differ significantly based on the
+available bus technology, capability of the host CPU and mainboard,
+the wiring of the buses and whether switches are used to increase the
+number of available bus slots, or if GPUs are housed in an external
+enclosure.  This can become quite complex. :l
+
+To achieve significant acceleration through GPUs, both KOKKOS and GPU
+package require capable GPUs with fast on-device memory and efficient
+data transfer rates. This requests capable upper mid-level to high-end
+(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
+result in a slowdown instead. :l
+
+For the GPU package, specifically when running in parallel with MPI,
+if it often more efficient to exclude the PPPM kspace style from GPU
+acceleration and instead run it - concurrently with a GPU accelerated
+pair style - on the CPU. This can often be easily achieved with placing
+a {suffix off} command before and a {suffix on} command after the
+{kspace_style pppm} command. :l
+
+The KOKKOS/OpenMP and USER-OMP package have different thread management
+strategies, which should result in USER-OMP being more efficient for a
+small number of threads with increasing overhead as the number of threads
+per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
+case, but have lower performance with few threads. :l
+
+The USER-INTEL package contains many options and settings for achieving
+additional performance on Intel hardware (CPU and accelerator cards), but
+to unlock this potential, an Intel compiler is required. The package code
+will compile with GNU gcc, but it will not be as efficient. :l
 :ule
 
-[Differences between the two packages:]
+[Differences between the GPU and KOKKOS packages:]
 
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations. :ulb,l
+The GPU package accelerates only pair force, neighbor list, and (parts
+of) PPPM calculations. The KOKKOS package attempts to run most of the
+calculation on the GPU, but can transparently support non-accelerated
+code (with a performance penalty due to having data transfers between
+host and GPU). :ulb,l
 
 The GPU package requires neighbor lists to be built on the CPU when using
 exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+
+The GPU package can be compiled for CUDA or OpenCL and thus supports
+both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
+resulting in equal or better performance over OpenCL. :l
+
+OpenCL in the GPU package does theoretically also support Intel CPUs or
+Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
+is superior. :l
 :ule

doc/src/Speed_gpu.txt

@@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 GPU package :h3
 
-The GPU package was developed by Mike Brown at ORNL and his
-collaborators, particularly Trung Nguyen (ORNL).  It provides GPU
-versions of many pair styles, including the 3-body Stillinger-Weber
-pair style, and for "kspace_style pppm"_kspace_style.html for
-long-range Coulombics.  It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+"kspace_style pppm"_kspace_style.html for long-range Coulombics.
+It has the following general features:
 
 It is designed to exploit common GPU hardware configurations where one
 or more GPUs are coupled to many cores of one or more multi-core CPUs,
 e.g. within a node of a parallel machine. :ulb,l
 
-Atom-based data (e.g. coordinates, forces) moves back-and-forth
+Atom-based data (e.g. coordinates, forces) are moved back-and-forth
 between the CPU(s) and GPU every timestep. :l
 
 Neighbor lists can be built on the CPU or on the GPU :l
@@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
 run on the GPU.  The FFT portion, which requires MPI communication
 between processors, runs on the CPU. :l
 
-Asynchronous force computations can be performed simultaneously on the
-CPU(s) and GPU. :l
+Force computations of different style (pair vs. bond/angle/dihedral/improper)
+can be performed concurrently on the GPU and CPU(s), respectively. :l
 
 It allows for GPU computations to be performed in single or double
 precision, or in mixed-mode precision, where pairwise forces are
@@ -39,21 +39,32 @@ force vectors. :l
 LAMMPS-specific code is in the GPU package.  It makes calls to a
 generic GPU library in the lib/gpu directory.  This library provides
 NVIDIA support as well as more general OpenCL support, so that the
-same functionality can eventually be supported on a variety of GPU
-hardware. :l
+same functionality is supported on a variety of hardware. :l
 :ule
 
 [Required hardware/software:]
 
-To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA CUDA software on your system:
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
 
-Check if you have an NVIDIA GPU: cat
-/proc/driver/nvidia/gpus/0/information Go to
-http://www.nvidia.com/object/cuda_get.html Install a driver and
-toolkit appropriate for your system (SDK is not necessary) Run
-lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
-below) to list supported devices and properties :ul
+Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
+Go to http://www.nvidia.com/object/cuda_get.html :l
+Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
+Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
+list supported devices and properties :ule,l
+
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
+Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
+installed. There can be multiple of them for the same or different hardware
+(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
+as 'platforms'.  The GPU library will select the [first] suitable platform,
+but this can be overridded using the device option of the "package"_package.html
+command. run lammps/lib/gpu/ocl_get_devices to get a list of available
+platforms and devices with a suitable ICD available.
 
 [Building LAMMPS with the GPU package:]
 
@@ -120,7 +131,10 @@ GPUs/node to use, as well as other options.
 
 The performance of a GPU versus a multi-core CPU is a function of your
 hardware, which pair style is used, the number of atoms/GPU, and the
-precision used on the GPU (double, single, mixed).
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
 
 See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
 LAMMPS web site for performance of the GPU package on various
@@ -146,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
 performance.  Neighbor lists can be built on the GPU or CPU.  Force
 calculations can be dynamically balanced across the CPU cores and
 GPUs.  GPU-specific settings can be made which can be optimized
-for different hardware.  See the "packakge"_package.html command
+for different hardware.  See the "package"_package.html command
 doc page for details. :l
 
 As described by the "package gpu"_package.html command, GPU

doc/src/Tools.txt

@@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
 reside in that directory.  Most of them are larger packages in their
 own sub-directories with their own Makefiles and/or README files.
 
-"amber2lmp"_#amber
-"binary2txt"_#binary
-"ch2lmp"_#charmm
-"chain"_#chain
-"colvars"_#colvars
-"createatoms"_#createatoms
-"doxygen"_#doxygen
-"drude"_#drude
-"eam database"_#eamdb
-"eam generate"_#eamgn
-"eff"_#eff
-"emacs"_#emacs
-"fep"_#fep
-"i-pi"_#ipi
-"ipp"_#ipp
-"kate"_#kate
-"lmp2arc"_#arc
-"lmp2cfg"_#cfg
-"matlab"_#matlab
-"micelle2d"_#micelle
-"moltemplate"_#moltemplate
-"msi2lmp"_#msi
-"phonon"_#phonon
-"polybond"_#polybond
-"pymol_asphere"_#pymol
-"python"_#pythontools
-"reax"_#reax_tool
-"smd"_#smd
-"vim"_#vim
-"xmgrace"_#xmgrace :ul
+:line
+
+Pre-processing tools :h3
+
+"amber2lmp"_#amber,
+"ch2lmp"_#charmm,
+"chain"_#chain,
+"createatoms"_#createatoms,
+"drude"_#drude,
+"eam database"_#eamdb,
+"eam generate"_#eamgn,
+"eff"_#eff,
+"ipp"_#ipp,
+"micelle2d"_#micelle,
+"moltemplate"_#moltemplate,
+"msi2lmp"_#msi,
+"polybond"_#polybond :tb(c=6,ea=c,a=l)
+
+Post-processing tools :h3
+
+"amber2lmp"_#amber,
+"binary2txt"_#binary,
+"ch2lmp"_#charmm,
+"colvars"_#colvars,
+"eff"_#eff,
+"fep"_#fep,
+"lmp2arc"_#arc,
+"lmp2cfg"_#cfg,
+"matlab"_#matlab,
+"phonon"_#phonon,
+"pymol_asphere"_#pymol,
+"python"_#pythontools,
+"reax"_#reax_tool,
+"smd"_#smd,
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+
+Miscellaneous tools :h3
+
+"doxygen"_#doxygen,
+"emacs"_#emacs,
+"i-pi"_#ipi,
+"kate"_#kate,
+"vim"_#vim :tb(c=5,ea=c,a=l)
 
 :line
 
-amber2lmp tool :h3,link(amber)
+Tool descriptions :h3
+
+amber2lmp tool :h4,link(amber)
 
 The amber2lmp sub-directory contains two Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
@@ -91,7 +106,7 @@ necessary modifications yourself.
 
 :line
 
-binary2txt tool :h3,link(binary)
+binary2txt tool :h4,link(binary)
 
 The file binary2txt.cpp converts one or more binary LAMMPS dump file
 into ASCII text files.  The syntax for running the tool is
@@ -104,7 +119,7 @@ since binary files are not compatible across all platforms.
 
 :line
 
-ch2lmp tool :h3,link(charmm)
+ch2lmp tool :h4,link(charmm)
 
 The ch2lmp sub-directory contains tools for converting files
 back-and-forth between the CHARMM MD code and LAMMPS.
@@ -129,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
 
 :line
 
-chain tool :h3,link(chain)
+chain tool :h4,link(chain)
 
 The file chain.f creates a LAMMPS data file containing bead-spring
 polymer chains and/or monomer solvent atoms.  It uses a text file
@@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.html.
 
 :line
 
-colvars tools :h3,link(colvars)
+colvars tools :h4,link(colvars)
 
 The colvars directory contains a collection of tools for postprocessing
 data produced by the colvars collective variable library.
@@ -168,7 +183,7 @@ gmail.com) at ICTP, Italy.
 
 :line
 
-createatoms tool :h3,link(createatoms)
+createatoms tool :h4,link(createatoms)
 
 The tools/createatoms directory contains a Fortran program called
 createAtoms.f which can generate a variety of interesting crystal
@@ -181,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
 
 :line
 
-doxygen tool :h3,link(doxygen)
+doxygen tool :h4,link(doxygen)
 
 The tools/doxygen directory contains a shell script called
 doxygen.sh which can generate a call graph and API lists using
@@ -193,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
 
 :line
 
-drude tool :h3,link(drude)
+drude tool :h4,link(drude)
 
 The tools/drude directory contains a Python script called
 polarizer.py which can add Drude oscillators to a LAMMPS
@@ -206,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
 
 :line
 
-eam database tool :h3,link(eamdb)
+eam database tool :h4,link(eamdb)
 
 The tools/eam_database directory contains a Fortran program that will
 generate EAM alloy setfl potential files for any combination of 16
@@ -222,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
 
 :line
 
-eam generate tool :h3,link(eamgn)
+eam generate tool :h4,link(eamgn)
 
 The tools/eam_generate directory contains several one-file C programs
 that convert an analytic formula into a tabulated "embedded atom
@@ -235,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
 
 :line
 
-eff tool :h3,link(eff)
+eff tool :h4,link(eff)
 
 The tools/eff directory contains various scripts for generating
 structures and post-processing output for simulations using the
@@ -246,7 +261,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
 
 :line
 
-emacs tool :h3,link(emacs)
+emacs tool :h4,link(emacs)
 
 The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs 
 that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -257,7 +272,7 @@ These tools were provided by Aidan Thompson at Sandia
 
 :line
 
-fep tool :h3,link(fep)
+fep tool :h4,link(fep)
 
 The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
@@ -270,7 +285,7 @@ See README file in the tools/fep directory.
 
 :line
 
-i-pi tool :h3,link(ipi)
+i-pi tool :h4,link(ipi)
 
 The tools/i-pi directory contains a version of the i-PI package, with
 all the LAMMPS-unrelated files removed.  It is provided so that it can
@@ -287,7 +302,7 @@ calculations with LAMMPS.
 
 :line
 
-ipp tool :h3,link(ipp)
+ipp tool :h4,link(ipp)
 
 The tools/ipp directory contains a Perl script ipp which can be used
 to facilitate the creation of a complicated file (say, a lammps input
@@ -301,7 +316,7 @@ tools/createatoms tool's input file.
 
 :line
 
-kate tool :h3,link(kate)
+kate tool :h4,link(kate)
 
 The file in the tools/kate directory is an add-on to the Kate editor
 in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -312,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio
 
 :line
 
-lmp2arc tool :h3,link(arc)
+lmp2arc tool :h4,link(arc)
 
 The lmp2arc sub-directory contains a tool for converting LAMMPS output
 files to the format for Accelrys' Insight MD code (formerly
@@ -328,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
 
 :line
 
-lmp2cfg tool :h3,link(cfg)
+lmp2cfg tool :h4,link(cfg)
 
 The lmp2cfg sub-directory contains a tool for converting LAMMPS output
 files into a series of *.cfg files which can be read into the
@@ -339,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 :line
 
-matlab tool :h3,link(matlab)
+matlab tool :h4,link(matlab)
 
 The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
 post-processing LAMMPS output.  The scripts include readers for log
@@ -357,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
 
 :line
 
-micelle2d tool :h3,link(micelle)
+micelle2d tool :h4,link(micelle)
 
 The file micelle2d.f creates a LAMMPS data file containing short lipid
 chains in a monomer solution.  It uses a text file containing lipid
@@ -374,7 +389,7 @@ definition file.  This tool was used to create the system for the
 
 :line
 
-moltemplate tool :h3,link(moltemplate)
+moltemplate tool :h4,link(moltemplate)
 
 The moltemplate sub-directory contains a Python-based tool for
 building molecular systems based on a text-file description, and
@@ -388,7 +403,7 @@ supports it.  It has its own WWW page at
 
 :line
 
-msi2lmp tool :h3,link(msi)
+msi2lmp tool :h4,link(msi)
 
 The msi2lmp sub-directory contains a tool for creating LAMMPS template
 input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -405,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information.
 
 :line
 
-phonon tool :h3,link(phonon)
+phonon tool :h4,link(phonon)
 
 The phonon sub-directory contains a post-processing tool useful for
 analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -420,7 +435,7 @@ University.
 
 :line
 
-polybond tool :h3,link(polybond)
+polybond tool :h4,link(polybond)
 
 The polybond sub-directory contains a Python-based tool useful for
 performing "programmable polymer bonding".  The Python file
@@ -434,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
 
 :line
 
-pymol_asphere tool :h3,link(pymol)
+pymol_asphere tool :h4,link(pymol)
 
 The pymol_asphere sub-directory contains a tool for converting a
 LAMMPS dump file that contains orientation info for ellipsoidal
@@ -452,7 +467,7 @@ This tool was written by Mike Brown at Sandia.
 
 :line
 
-python tool :h3,link(pythontools)
+python tool :h4,link(pythontools)
 
 The python sub-directory contains several Python scripts
 that perform common LAMMPS post-processing tasks, such as:
@@ -468,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts.
 
 :line
 
-reax tool :h3,link(reax_tool)
+reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alond codes that can
 post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -479,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia.
 
 :line
 
-smd tool :h3,link(smd)
+smd tool :h4,link(smd)
 
 The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
 Makefile which can be compiled and used to convert triangle output
@@ -495,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 
 :line
 
-vim tool :h3,link(vim)
+vim tool :h4,link(vim)
 
 The files in the tools/vim directory are add-ons to the VIM editor
 that allow easier editing of LAMMPS input scripts.  See the README.txt
@@ -506,7 +521,7 @@ ziegenhain.com)
 
 :line
 
-xmgrace tool :h3,link(xmgrace)
+xmgrace tool :h4,link(xmgrace)
 
 The files in the tools/xmgrace directory can be used to plot the
 thermodynamic data in LAMMPS log files via the xmgrace plotting

doc/src/compute_pair.txt

@@ -27,7 +27,9 @@ compute 1 all pair reax :pre
 
 Define a computation that extracts additional values calculated by a
 pair style, and makes them accessible for output or further processing
-by other commands.  The group specified for this command is ignored.
+by other commands.
+
+NOTE: The group specified for this command is [ignored].
 
 The specified {pstyle} must be a pair style used in your simulation
 either by itself or as a sub-style in a "pair_style hybrid or

doc/src/fix_bond_react.txt

@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
 modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
 identified: if the bonding atoms in the pre-reacted template are not
 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
 its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
 nearest bonding partners, these two atoms are identified as the
 bonding atom pair of the reaction site. Once this unique bonding atom
 pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
 
 [Default:]
 
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
 
 :line
 

doc/src/lammps.book

@@ -25,7 +25,8 @@ Build_basics.html
 Build_settings.html
 Build_package.html
 Build_extras.html
-Run.html
+Build_windows.html
+Run_head.html
 Run_basics.html
 Run_options.html
 Run_output.html

lib/latte/Makefile.lammps.ifort

@@ -4,9 +4,9 @@
 
 latte_SYSINC = 
 latte_SYSLIB = ../../lib/latte/filelink.o \
-               -llatte -lifcore -lsvml -lompstub -limf -lmkl_intel_lp64 \
-               -lmkl_intel_thread -lmkl_core -lmkl_intel_thread -lpthread \
-               -openmp -O0
+               -llatte -lifport -lifcore -lsvml -lompstub -limf \
+               -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core \
+               -lmkl_intel_thread -lpthread -openmp
 latte_SYSPATH = -openmp -L${MKLROOT}/lib/intel64 -lmkl_lapack95_lp64 \
                 -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64
 

python/lammps.py

@@ -173,6 +173,9 @@ class lammps(object):
         self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
 
       else:
+        if lammps.has_mpi4py:
+          from mpi4py import MPI
+          self.comm = MPI.COMM_WORLD
         self.opened = 1
         if cmdargs:
           cmdargs.insert(0,"lammps.py")
@@ -862,6 +865,10 @@ class PyLammps(object):
 
   def run(self, *args, **kwargs):
     output = self.__getattr__('run')(*args, **kwargs)
+
+    if(lammps.has_mpi4py):
+      output = self.lmp.comm.bcast(output, root=0) 
+    
     self.runs += get_thermo_data(output)
     return output
 

src/USER-COLVARS/fix_colvars.h

@@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars)
 #define LMP_FIX_COLVARS_H
 
 #include "fix.h"
-#include <vector>
 
 // forward declaration
 class colvarproxy_lammps;
@@ -77,13 +76,6 @@ class FixColvars : public Fix {
   int   num_coords;    // total number of atoms controlled by this fix
   tagint *taglist;     // list of all atom IDs referenced by colvars.
 
-  // TODO get rid of these
-  // std::vector<cvm::atom_pos> *coords; // coordinates of colvar atoms
-  // std::vector<cvm::rvector> *forces; // received forces of colvar atoms
-  // std::vector<cvm::rvector> *oforce; // old total forces of colvar atoms
-  // std::vector<cvm::real> *masses;
-  // std::vector<cvm::real> *charges;
-
   int   nmax;          // size of atom communication buffer.
   int   size_one;      // bytes per atom in communication buffer.
   struct commdata *comm_buf; // communication buffer

src/USER-MISC/fix_bond_react.cpp

@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
         hang_catch++;
         // let's go ahead and catch the simplest of hangs
         //if (hang_catch > onemol->natoms*4)
-        if (hang_catch > atom->nlocal*3) {
-          error->all(FLERR,"Excessive iteration of superimpose algorithm");
+        if (hang_catch > atom->nlocal*30) {
+          error->one(FLERR,"Excessive iteration of superimpose algorithm");
         }
       }
     }
@@ -1554,6 +1554,40 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
       error->one(FLERR,"Atom affected by reaction too close to template edge");
   }
 
+  // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+  // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
+  for (int i = 0; i < twomol->natoms; i++) {
+    if (landlocked_atoms[i][myrxn] == 0) {
+      int twomol_atomi = i+1;
+      for (int j = 0; j < twomol->num_bond[i]; j++) {
+        int twomol_atomj = twomol->bond_atom[i][j];
+        if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
+          int onemol_atomi = equivalences[i][1][myrxn];
+          int onemol_batom;
+          for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+            onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+            if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+              if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+                error->one(FLERR,"Bond type affected by reaction too close to template edge");
+              }
+            }
+          }
+          if (newton_bond) {
+            int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+            for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+              onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+              if (onemol_batom == equivalences[i][1][myrxn]) {
+                if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+                  error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
   // also, if atoms change number of bonds, but aren't landlocked, that could be bad
   if (me == 0)
     for (int i = 0; i < twomol->natoms; i++) {
@@ -2067,7 +2101,7 @@ void FixBondReact::update_everything()
                   nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
                   nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
                 }
-                for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+                for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
                   special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
                 }
                 special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Aug 2018"
+#define LAMMPS_VERSION "22 Aug 2018"