Merge branch 'master' into collected-small-changes

cmake/CMakeLists.txt

@@ -496,10 +496,44 @@ if(BUILD_LIB)
   if(LAMMPS_DEPS)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
+  set(LAMMPS_CXX_HEADERS
+    angle.h
+    atom.h
+    bond.h
+    citeme.h
+    comm.h
+    compute.h
+    dihedral.h
+    domain.h
+    error.h
+    fix.h
+    force.h
+    group.h
+    improper.h
+    input.h
+    kspace.h
+    lammps.h
+    lattice.h
+    lmppython.h
+    memory.h
+    modify.h
+    neighbor.h
+    neigh_list.h
+    output.h
+    pair.h
+    pointers.h
+    region.h
+    timer.h
+    universe.h
+    update.h
+    variable.h)
+  list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/)
+
   set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
   install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
@@ -550,11 +584,11 @@ include(Documentation)
 ###############################################################################
 # Install potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
-install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR})
+install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
-
+if(BUILD_TOOLS)
-set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
-install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR})
+endif()
 
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)

cmake/Modules/Packages/KIM.cmake

@@ -9,6 +9,9 @@ if(PKG_KIM)
   if(KIM-API_FOUND)
     set(DOWNLOAD_KIM_DEFAULT OFF)
   else()
+    if (NOT DOWNLOAD_KIM)
+      message(WARNING "KIM-API package not found.  We will download and build our own")
+    endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
   option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
@@ -21,8 +24,8 @@ if(PKG_KIM)
     enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
-      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      URL_MD5 6ac52e14ef52967fc7858220b208cba5
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

cmake/etc/profile.d/lammps.csh.in

@@ -1,4 +1,4 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
-if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

cmake/etc/profile.d/lammps.sh.in

@@ -1,5 +1,5 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
-MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
 export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

doc/include-file-conventions.md

@@ -0,0 +1,133 @@
+# Outline of include file conventions in LAMMPS
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what include files
+and definitions to put where into LAMMPS source.
+Last change 2019-07-05
+
+## Table of Contents
+
+  * [Motivation](#motivation)
+  * [Rules](#rules)
+  * [Tools](#tools)
+  * [Legacy Code](#legacy-code)
+
+## Motivation
+
+The conventions outlined in this document are supposed to help make
+maintenance of the LAMMPS software easier.  By trying to achieve
+consistency across files contributed by different developers, it will
+become easier for the code maintainers to modify and adjust files and,
+overall, the chance for errors or portability issues will be reduced.
+The rules employed are supposed to minimize naming conflicts and
+simplify dependencies between files and thus speed up compilation. They
+may, as well, make otherwise hidden dependencies visible.
+
+## Rules
+
+Below are the various rules that are applied.  Not all are enforced
+strictly and automatically.  If there are no significant side effects,
+exceptions may be possible for cases where a full compliance to the
+rules may require a large effort compared to the benefit.
+
+### Core Files Versus Package Files
+
+All rules listed below are most strictly observed for core LAMMPS files,
+which are the files that are not part of a package, and the files of the
+packages MOLECULE, MANYBODY, KSPACE, and RIGID.  On the other end of
+the spectrum are USER packages and legacy packages that predate these
+rules and thus may not be fully compliant.  Also, new contributions
+will be checked more closely, while existing code will be incrementally
+adapted to the rules as time and required effort permits.
+
+### System Versus Local Header Files
+
+All system- or library-provided include files are included with angular
+brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
+include files provided with LAMMPS are included with double quotes
+(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
+
+For headers declaring functions of the C-library, the corresponding
+C++ versions should be included (examples: `#include <cstdlib>` or
+`#include <cctypes>`).  However, these includes are limited to those defined
+in the C++98 standard.  Some files thus must use the older style until
+the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
+even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### C++ Standard Compliance
+
+LAMMPS core files currently correspond to the C++98 standard. Files
+requiring C++11 or later are only permitted in (optional) packages
+and particularly packages that are not part of the list of commonly
+used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+
+Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
+Since using both at the same time can cause problems, iostreams should
+be avoided where possible.
+
+### Lean Header Files
+
+Header files will typically contain the definition of a (single) class.
+These header files should have as few include statements as possible.
+This is particularly important for classes that implement a "style" and
+thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
+all be included in the auto-generated `"some_style.h"` files which 
+results in a high potential for direct or indirect symbol name clashes.
+
+In the ideal case, the header would only include one file defining the
+parent class. That would typically be either `#include "pointers.h"` for
+the `Pointers` class, or a header of a class derived from it like
+`#include "pair.h"` for the `Pair` class and so on.  References to other
+classes inside the class should be make through pointers, for which forward
+declarations (inside the `LAMMPS_NS` or the new class' namespace) can
+be employed.  The full definition will then be included into the corresponding
+implementation file.  In the given example from above, the header file
+would be called `some_name.h` and the implementation `some_name.cpp` (all
+lower case with underscores, while the class itself would be in camel case
+and no underscores `SomeName`, and the style name with lower case names separated by
+a forward slash).
+
+### Implementation Files
+
+In the implementation files (typically, those would have the same base name
+as the corresponding header with a .cpp extension instead of .h) include
+statements should follow the "include what you use" principle.
+
+### Order of Include Statements
+
+Include files should be included in this order:
+* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
+* mpi.h
+* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* LAMMPS local headers (preferably in alphabetical order)
+
+### Special Cases and Exceptions
+
+#### pointers.h
+
+The `pointer.h` header file also includes `cstdio` and `lmptype.h`
+(and through it `stdint.h`, `intttypes.h`, and `climits`).
+This means any header including `pointers.h` can assume that `FILE`,
+`NULL`, `INT_MAX` are defined.
+
+## Tools
+
+The [Include What You Use tool](https://include-what-you-use.org/)
+can be used to provide supporting information about compliance with
+the rules listed here.  There are some limitations and the IWYU tool
+may give incorrect advice.  The tools is activated by setting the
+CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+path of the `include-what-you-use` command.  When activated, the
+tool will be run after each compilation and provide suggestions for
+which include files should be added or removed.
+
+## Legacy Code
+
+A lot of code predates the application of the rules in this document
+and the rules themselves are a moving target.  So there are going to be
+significant chunks of code that do not fully comply.  This applies
+for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+developers are dedicated to make an effort to improve the compliance
+and welcome volunteers wanting to help with the process.
+

doc/src/Build_cmake.txt

@@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up repeated compilation
 even more.
 
-After compilation, you can optionally copy the LAMMPS executable and
+After compilation, you may optionally install the LAMMPS executable into
-library into your system folders (by default under $HOME/.local) with:
+your system with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
+to $\{HOME\}/.local
+
 :line
 
 There are 3 variants of CMake: a command-line version (cmake), a text mode

doc/src/Build_extras.txt

@@ -172,22 +172,17 @@ KIM package :h4,link(kim)
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
-element or alloy and set of parameters, e.g. EAM for Cu with a
+See the list of all KIM models here: https://openkim.org/browse/models
-specific EAM potential file.  Also note that downloading and installing
-the KIM API library with all its models, may take a long time (10s of
-minutes to hours) to build.  Of course you only need to do that once.
 
-See the list of KIM model drivers here:
+(Also note that when downloading and installing from source
-https://openkim.org/browse/model-drivers/alphabetical
+the KIM API library with all its models, may take a long time (tens of
-
+minutes to hours) to build.  Of course you only need to do that once.)
-See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
 
 [CMake build]:
 

doc/src/Commands_all.txt

@@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
-"kim_query"_kim_query.html,
+"kim_init"_kim_commands.html,
+"kim_interactions"_kim_commands.html,
+"kim_query"_kim_commands.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,

doc/src/Commands_compute.txt

@@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
+"gyration/shape"_compute_gyration_shape.html,
 "heat/flux"_compute_heat_flux.html,
 "heat/flux/tally"_compute_tally.html,
 "hexorder/atom"_compute_hexorder_atom.html,
@@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "meso/e/atom"_compute_meso_e_atom.html,
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
+"momentum"_compute_momentum.html,
 "msd"_compute_msd.html,
 "msd/chunk"_compute_msd_chunk.html,
 "msd/nongauss"_compute_msd_nongauss.html,

doc/src/Eqs/compute_shape_parameters.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ c = l_z - 0.5(l_y+l_x) \\
+ b = l_y - l_x \\
+ k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Errors_messages.txt

@@ -2438,6 +2438,14 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Compute gyration ID does not exist for compute gyration/shape} :dt
+
+Self-explanatory. Provide a valid compute ID. :dd
+
+{Compute gyration/shape compute ID does not point to a gyration compute} :dt
+
+Self-explanatory. Provide and ID of a compute gyration command. :dd
+
 {Compute ID for compute reduce does not exist} :dt
 
 Self-explanatory. :dd
@@ -5777,6 +5785,16 @@ definitions. :dd
 
 The data file header lists improper but no improper types. :dd
 
+{Incompatible KIM Simulator Model} :dt
+
+The requested KIM Simulator Model was defined for a different MD code
+and thus is not compatible with LAMMPS. :dd
+
+{Incompatible units for KIM Simulator Model} :dt
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model. :dd
+
 {Incomplete use of variables in create_atoms command} :dt
 
 The var and set options must be used together. :dd
@@ -7047,6 +7065,12 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
+{KIM Simulator Model has no Model definition} :dt
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this. :dd
+
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -7551,6 +7575,18 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Must use 'kim_style init' command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style define' command after simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style init' command before 'kim_style define'} :dt
+
+Self-explanatory. :dd
+
 {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt
 
 The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd
@@ -9494,6 +9530,11 @@ See the "read_data extra/special/per/atom" command
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 
+{Species XXX is not supported by this KIM Simulator Model} :dt
+
+The kim_style define command was referencing a species that is not
+present in the requested KIM Simulator Model. :dd
+
 {Specified processors != physical processors} :dt
 
 The 3d grid of processors defined by the processors command does not

doc/src/Errors_warnings.txt

@@ -129,6 +129,16 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt
+
+The communication cutoff defaults to the maximum of what is inferred from
+pair and bond styles (will be zero, if none are defined) and what is specified
+via "comm_modify cutoff"_comm_modify.html (defaults to 0.0).  If this results
+to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+incorrect periodic images of atoms in interaction lists.  To avoid, either use
+"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify
+cutoff"_comm_modify.html. :dd
+
 {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
 
 Self-explanatory. :dd

doc/src/Examples.txt

@@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+kim:      use of potentials from the "OpenKIM Repository"_openkim
 latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
@@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
 instructions.  See the "Packages_details"_Packages_details.html doc
 page for more info on specific USER packages.
+
+:link(openkim,https://openkim.org)

doc/src/Install_mac.txt

@@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Download an executable for Mac :h3
 
 LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-"Homebrew"_homebrew.  Only four of the LAMMPS packages are unavailable
+"Homebrew"_homebrew.  The following LAMMPS packages are unavailable at this
-at this time because of additional needs not yet met: KIM, GPU,
+time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
-USER-INTEL, USER-ATC.
+MESSAGE, MPIIO POEMS VORONOI.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:
 
-% brew tap homebrew/science
+% brew install lammps :pre
-% brew install lammps              # serial version
-% brew install lammps --with-mpi   # mpi support :pre
 
-This will install the executable "lammps", a python module named
+This will install the executables "lammps_serial" and "lammps_mpi", as well as
-"lammps", and additional resources with all the standard packages.  To
+the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
-get the location of the additional resources type this:
-
-% brew info lammps :pre
-
-This command also tells you additional installation options available.
-The user-packages are available as options, just install them like
-this example for the USER-OMP package:
-
-% brew install lammps --enable-user-omp :pre
-
-It is usually best to install LAMMPS with the most up to date source
-files, which can be done with the "--HEAD" option:
-
-% brew install lammps --HEAD :pre
-
-To re-install the LAMMPS HEAD, run this command occasionally (make sure
-to use the desired options).
-
-% brew install --force lammps --HEAD $\{options\} :pre
 
 Once LAMMPS is installed, you can test the installation with the
 Lennard-Jones benchmark file:
 
 % brew test lammps -v :pre
 
+The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
+results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from "openkim.org"_openkim, you can
+install the `openkim-models` package
+
+% brew install openkim-models :pre
+
 If you have problems with the installation you can post issues to
 "this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
-:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)
+:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
+:link(openkim,https://openkim.org)

doc/src/Intro_features.txt

@@ -92,8 +92,8 @@ commands)
   implicit solvent potentials: hydrodynamic lubrication, Debye
   force-field compatibility with common CHARMM, AMBER, DREIDING, \
     OPLS, GROMACS, COMPASS options
-  access to "KIM archive"_http://openkim.org of potentials via \
+  access to the "OpenKIM Repository"_http://openkim.org of potentials via \
-    "pair kim"_pair_kim.html
+    "kim_init, kim_interactions, and kim_query"_kim_commands.html commands
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
     potentials can be used in one simulation
   overlaid potentials: superposition of multiple pair potentials :ul

doc/src/Packages_details.txt

@@ -338,22 +338,37 @@ KIM package :link(PKG-KIM),h4
 
 [Contents:]
 
-A "pair_style kim"_pair_kim.html command which is a wrapper on the
+This package contains a set of commands that serve as a wrapper on the
-Knowledge Base for Interatomic Models (KIM) repository of interatomic
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
-potentials, enabling any of them to be used in LAMMPS simulations.
+repository of interatomic models (IMs)
-Also a "kim_query"_kim_query.html command, which allows to query
+enabling compatible ones to be used in LAMMPS simulations.
-the OpenKIM database for stored properties.
+This includes "kim_init and kim_interactions"_kim_commands.html
+commands to select, initialize and instantiate the IM, and a
+"kim_query"_kim_commands.html command to perform web queries
+for material property predictions of OpenKIM IMs.
+Support for KIM IMs that conform to the
+"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
+is provided by the "pair_style kim"_pair_kim.html command.
 
-To use this package you must have the KIM library available on your
+NOTE: The command {pair_style kim} is called by {kim_interactions} and
-system.
+is not recommended to be directly used in input scripts.
+
+To use this package you must have the KIM API library available on your
+system. The KIM API is available for download on the
+"OpenKIM website"_https://openkim.org/kim-api/.
+When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed.
 
 Information about the KIM project can be found at its website:
-https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
+"https://openkim.org"_https://openkim.org.
-Elliott (U Minnesota).
+The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
+and is funded by the "National Science Foundation"_https://www.nsf.gov/.
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API which the "pair_style kim"_pair_kim.html command uses.  He
+API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
-developed the pair style.
+Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
+interface in close collaboration with Ryan Elliott.
+
 
 [Install:]
 
@@ -363,10 +378,11 @@ extras"_Build_extras.html doc page.
 
 [Supporting info:]
 
+"kim_commands"_kim_commands.html
+"pair_style kim"_pair_kim.html
 src/KIM: filenames -> commands
 src/KIM/README
 lib/kim/README
-"pair_style kim"_pair_kim.html
 examples/kim :ul
 
 :line
@@ -984,9 +1000,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4
 
 [Contents:]
 
-ADIOS is a high-performance I/O library. This package implements the 
+ADIOS is a high-performance I/O library. This package implements the
 dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library. 
+the ADIOS library.
 
 [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
 

doc/src/comm_modify.txt

@@ -69,9 +69,15 @@ processors.  By default the ghost cutoff = neighbor cutoff = pairwise
 force cutoff + neighbor skin.  See the "neighbor"_neighbor.html command
 for more information about the skin distance.  If the specified Rcut is
 greater than the neighbor cutoff, then extra ghost atoms will be acquired.
-If the provided cutoff is smaller, the provided value will be ignored
+If the provided cutoff is smaller, the provided value will be ignored,
-and the ghost cutoff is set to the neighbor cutoff. Specifying a
+the ghost cutoff is set to the neighbor cutoff and a warning will be
-cutoff value of 0.0 will reset any previous value to the default.
+printed. Specifying a cutoff value of 0.0 will reset any previous value
+to the default. If bonded interactions exist and equilibrium bond length
+information is available, then also a heuristic based on that bond length
+is computed. It is used as communication cutoff, if there is no pair
+style present and no {comm_modify cutoff} command used. Otherwise a
+warning is printed, if this bond based estimate is larger than the
+communication cutoff used. A
 
 The {cutoff/multi} option is equivalent to {cutoff}, but applies to
 communication mode {multi} instead. Since in this case the communication

doc/src/commands_list.txt

@@ -53,7 +53,7 @@ Commands :h1
    include
    info
    jump
-   kim_query
+   kim_commands
    kspace_modify
    kspace_style
    label

doc/src/compute.txt

@@ -177,7 +177,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "angle"_compute_angle.html - energy of each angle sub-style
 "angle/local"_compute_angle_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
-"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
+"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom
 "body/local"_compute_body_local.html - attributes of body sub-particles
 "bond"_compute_bond.html - energy of each bond sub-style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
@@ -213,6 +213,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
+"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
@@ -227,6 +228,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
 "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
 "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
+"momentum"_compute_momentum.html - translational momentum
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
 "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms

doc/src/compute_gyration.txt

@@ -67,6 +67,7 @@ distance^2 "units"_units.html respectively.
 
 [Related commands:]
 
-"compute gyration/chunk"_compute_gyration_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html,
+"compute gyration/shape"_compute_gyration_shape.html
 
 [Default:] none

doc/src/compute_gyration_shape.txt

@@ -0,0 +1,86 @@
+"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
+
+compute gyration/shape command :h3
+
+[Syntax:]
+
+compute ID group-ID gyration compute-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+gyration/shape = style name of this compute command
+compute-ID = ID of "compute gyration"_compute_gyration.html command :ul
+
+[Examples:]
+
+compute 1 molecule gyration/shape pe :pre
+
+[Description:]
+
+Define a computation that calculates the eigenvalues of the gyration tensor of a
+group of atoms and three shape parameters. The computation includes all effects
+due to atoms passing thru periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+:c,image(Eqs/compute_shape_parameters.jpg)
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+The asphericity  is always non-negative and zero only when the three principal
+moments are equal. This zero condition is met when the distribution of particles
+is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+NOTE: The coordinates of an atom contribute to the gyration tensor in
+"unwrapped" form, by using the image flags associated with each atom.
+See the "dump custom"_dump.html command for a discussion of "unwrapped"
+coordinates. See the Atoms section of the "read_data"_read_data.html
+command for a discussion of image flags and how they are set for each
+atom.  You can reset the image flags (e.g. to 0) before invoking this
+compute by using the "set image"_set.html command.
+
+[Output info:]
+
+This compute calculates a global vector of
+length 6, which can be accessed by indices 1-6. The first three values are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global  vector values from a compute as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are
+"intensive".  The first five vector values will be in
+distance^2 "units"_units.html while the sixth one is dimensionless.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute gyration"_compute_gyration.html
+
+[Default:] none
+
+:line
+
+:link(Theodorou)
+[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+

doc/src/compute_momentum.txt

@@ -0,0 +1,49 @@
+"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
+
+compute momentum command :h3
+
+[Syntax:]
+
+compute ID group-ID momentum :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+momentum = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all momentum :pre
+
+[Description:]
+
+Define a computation that calculates the translational momentum
+of a group of particles.
+
+The momentum of each particles is computed as m v, where m and v are
+the mass and velocity of the particle.
+
+[Output info:]
+
+This compute calculates a global vector (the summed momentum) of
+length 3. This value can be used by any command that uses a global
+vector value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector value calculated by this compute is "extensive". The vector
+value will be in mass*velocity "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+[Default:] none

doc/src/compute_pressure.txt

@@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command
 pressure = style name of this compute command
 temp-ID = ID of compute that calculates temperature, can be NULL if not needed
 zero or more keywords may be appended
-keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul
 
 [Examples:]
 
 compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond :pre
+compute 1 all pressure NULL pair bond
+compute 1 all pressure NULL pair/hybrid lj/cut :pre
 
 [Description:]
 
@@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.
 
+The {pair/hybrid} keyword means to only include contribution
+from a sub-style in a {hybrid} or {hybrid/overlay} pair style.
+
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for many-body potentials and accounting for the
 effects of periodic boundary conditions are discussed in

doc/src/computes.txt

@@ -44,6 +44,7 @@ Computes :h1
    compute_group_group
    compute_gyration
    compute_gyration_chunk
+   compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
    compute_improper
@@ -57,6 +58,7 @@ Computes :h1
    compute_meso_e_atom
    compute_meso_rho_atom
    compute_meso_t_atom
+   compute_momentum
    compute_msd
    compute_msd_chunk
    compute_msd_nongauss

doc/src/create_atoms.txt

@@ -242,9 +242,8 @@ write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-The {rotate} keyword can only be used with the {single} style and
+The {rotate} keyword allows specification of the orientation
-when adding a single molecule. It allows to specify the orientation
+at which molecules are inserted.  The axis of rotation is
-at which the molecule is inserted.  The axis of rotation is
 determined by the rotation vector (Rx,Ry,Rz) that goes through the
 insertion point.  The specified {theta} determines the angle of
 rotation around that axis.  Note that the direction of rotation for

doc/src/fix_adapt.txt

@@ -149,8 +149,7 @@ meaning of these parameters:
 "spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
 "table"_pair_table.html: table_cutoff: type pairs:
 "ufm"_pair_ufm.html: epsilon,sigma: type pairs:
-"soft"_pair_soft.html: a: type pairs:
+"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:)
-"kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
 
 NOTE: It is easy to add new pairwise potentials and their parameters
 to this list.  All it typically takes is adding an extract() method to

doc/src/fix_bond_react.txt

@@ -24,7 +24,7 @@ common_keyword = {stabilization} :l
   {stabilization} values = {no} or {yes} {group-ID} {xmax}
     {no} = no reaction site stabilization
     {yes} = perform reaction site stabilization
-      {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms
+      {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
       {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre
 react = mandatory argument indicating new reaction specification :l
   react-ID = user-assigned name for the reaction :l
@@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l
 
 [Examples:]
 
+For unabridged example scripts and files, see examples/USER/misc/bond_react.
+
 molecule mol1 pre_reacted_topology.txt
 molecule mol2 post_reacted_topology.txt
 fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
@@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should
 typically be set to the maximum distance that non-reacting atoms move
 during the simulation.
 
+Fix bond/react creates and maintains two important dynamic groups of
+atoms when using the {stabilization} keyword. The first group contains
+all atoms currently involved in a reaction; this group is
+automatically thermostatted by an internally-created
+"nve/limit"_fix_nve_limit.html integrator. The second group contains
+all atoms currently not involved in a reaction. This group should be
+used by a thermostat in order to time integrate the system. The name
+of this group of non-reacting atoms is created by appending '_REACT'
+to the group-ID argument of the {stabilization} keyword, as shown in
+the second example above.
+
+NOTE: When using reaction stabilization, you should generally not have
+a separate thermostat which acts on the 'all' group.
+
 The group-ID set using the {stabilization} keyword can be an existing
 static group or a previously-unused group-ID. It cannot be specified
 as 'all'. If the group-ID is previously unused, the fix bond/react
@@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic
 group is named by appending '_REACT' to the group-ID, e.g.
 nvt_grp_REACT. By specifying an existing group, you may thermostat
 constant-topology parts of your system separately. The dynamic group
-contains only non-reacting atoms at a given timestep, and therefore
+contains only atoms not involved in a reaction at a given timestep,
-should be used by a subsequent system-wide time integrator such as
+and therefore should be used by a subsequent system-wide time
-nvt, npt, or nve, as shown in the second example above. The time
+integrator such as nvt, npt, or nve, as shown in the second example
-integration command should be placed after the fix bond/react command
+above (full examples can be found at examples/USER/misc/bond_react).
-due to the internal dynamic grouping performed by fix bond/react.
+The time integration command should be placed after the fix bond/react
+command due to the internal dynamic grouping performed by fix
+bond/react.
 
 NOTE: If the group-ID is an existing static group, react-group-IDs
 should also be specified as this static group, or a subset.
 
-NOTE: If the group-ID is previously unused, the internally-created
-group applies to all atoms in the system, i.e. you should generally
-not have a separate thermostat which acts on the 'all' group, or any
-other group.
-
 The following comments pertain to each {react} argument (in other
 words, can be customized for each reaction, or reaction step):
 
@@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction
 by-products, this feature can be used to remove specific topologies,
 such as small rings, that may be otherwise indistinguishable.
 
-Also, it may be beneficial to ensure reacting atoms are at a certain
+Optionally, you can enforce additional behaviors on reacting atoms.
-temperature before being released to the overall thermostat. For this,
+For example, it may be beneficial to force reacting atoms to remain at
-you can use the internally-created dynamic group named
+a certain temperature. For this, you can use the internally-created
-"bond_react_MASTER_group." For example, adding the following command
+dynamic group named "bond_react_MASTER_group", which consists of all
-would thermostat the group of all atoms currently involved in a
+atoms currently involved in a reaction. For example, adding the
-reaction:
+following command would add an additional thermostat to the group of
+all currently-reacting atoms:
 
 fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
 

doc/src/kim_commands.txt

@@ -0,0 +1,522 @@
+"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
+
+kim_init command :h3
+kim_interactions command :h3
+kim_query command :h3
+
+[Syntax:]
+
+kim_init model user_units unitarg
+kim_interactions typeargs
+kim_query variable formatarg query_function queryargs :pre
+
+model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
+user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script
+unitarg = {unit_conversion_mode} (optional)
+typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping
+variable = name of a (string style) variable where the result of the query is stored
+formatarg = {split} (optional)
+query_function = name of the OpenKIM web API query function to be used
+queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul
+
+
+[Examples:]
+
+kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+kim_interactions Si
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
+kim_interactions C H O
+Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real
+kim_interactions fixed_types
+kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre
+
+[Description:]
+
+The set of {kim_commands} provide a high-level wrapper around the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs) (potentials and force fields),
+so that they can be used by LAMMPS scripts.  These commands do not implement
+any computations directly, but rather generate LAMMPS input commands based
+on the information retrieved from the OpenKIM repository to initialize and
+activate OpenKIM IMs and query their predictions for use in the LAMMPS script.
+All LAMMPS input commands generated and executed by {kim_commands} are
+echoed to the LAMMPS log file.
+
+Benefits of Using OpenKIM IMs :h4
+
+Employing OpenKIM IMs provides LAMMPS users with multiple benefits:
+
+Reliability :h5
+
+All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality.
+IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.
+IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the  "OpenKIM browse interface"_https://openkim.org/browse. :ul
+
+Reproducibility :h5
+
+Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits).  Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.
+OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul
+
+Convenience :h5
+
+IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page.
+The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis.
+Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units.  :ul
+
+:link(IM_types)
+Types of IMs in OpenKIM :h4
+
+There are two types of IMs archived in OpenKIM:
+
+The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/).
+The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol
+
+With these two IM types, OpenKIM can archive and test almost all IMs that
+can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see
+the "upload instructions"_https://openkim.org/doc/repository/adding-content/.)
+
+OpenKIM IMs are uniquely identified by a
+"KIM ID"_https://openkim.org/doc/schema/kim-ids/.
+The extended KIM ID consists of
+a human-readable prefix identifying the type of IM, authors, publication year,
+and supported species, separated by two underscores from the KIM ID itself,
+which begins with an IM code
+({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model)
+followed by a unique 12-digit code and a 3-digit version identifier.
+By convention SM prefixes begin with {Sim_} to readily identify them.
+
+SW_StillingerWeber_1985_Si__MO_405512056662_005
+Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre
+
+Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org
+providing all the information on the IM including a title, description,
+authorship and citation information, test and verification check results,
+visualizations of results, a wiki with documentation and user comments, and
+access to raw files, and other information.
+The URL for the Model Page is constructed from the
+"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM:
+
+https://openkim.org/id/extended_KIM_ID
+:pre
+
+For example for the Stillinger-Weber potential
+listed above the Model Page is located at:
+
+"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
+:pre
+
+See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species.
+This list is sorted by species and can be filtered to display only
+IMs for certain species combinations.
+
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+
+NOTE: It is also possible to locally install IMs not archived in OpenKIM,
+in which case their names do not have to conform to the KIM ID format.
+
+Using OpenKIM IMs with LAMMPS :h4
+
+Two commands are employed when using OpenKIM IMs, one to select the
+IM and perform necessary initialization ({kim_init}), and the second
+to set up the IM for use by executing any necessary LAMMPS commands
+({kim_interactions}). Both are required.
+
+See the {examples/kim} directory for example input scripts that use KIM PMs
+and KIM SMs.
+
+OpenKIM IM Initialization ({kim_init}) :h5
+
+The {kim_init} mode command must be issued [before]
+the simulation box is created (normally at the top of the file).
+This command sets the OpenKIM IM that will be used and may issue
+additional commands changing LAMMPS default settings that are required
+for using the selected IM (such as "units"_units.html or
+"atom_style"_atom_style.html). If needed, those settings can be overridden,
+however, typically a script containing a {kim_init} command
+would not include {units} and {atom_style} commands.
+
+The required arguments of {kim_init} are the {model} name of the
+IM to be used in the simulation (for an IM archived in OpenKIM this is
+its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and
+the {user_units}, which are the LAMMPS "units style"_units.html used
+in the input script.  (Any dimensioned numerical values in the input
+script and values read in from files are expected to be in the
+{user_units} system.)
+
+The selected IM can be either a "KIM PM or a KIM SM"_#IM_types.
+For a KIM SM, the {kim_init} command verifies that the SM is designed
+to work with LAMMPS (and not another simulation code).
+In addition, the LAMMPS version used for defining
+the SM and the LAMMPS version being currently run are
+printed to help diagnose any incompatible changes to input script or
+command syntax between the two LAMMPS versions.
+
+Based on the selected model {kim_init} may modify the
+"atom_style"_atom_style.html.
+Some SMs have requirements for this setting. If this is the case, then
+{atom_style} will be set to the required style. Otherwise, the value is left
+unchanged (which in the absence of an {atom_style} command in the input script
+is the "default atom_style value"_atom_style.html).
+
+Regarding units, the {kim_init} command behaves in different ways depending
+on whether or not {unit conversion mode} is activated as indicated by the
+optional {unitarg} argument.
+If unit conversion mode is [not] active, then {user_units} must
+either match the required units of the IM or the IM must be able
+to adjust its units to match. (The latter is only possible with some KIM PMs;
+SMs can never adjust their units.) If a match is possible, the LAMMPS
+"units"_units.html command is called to set the units to
+{user_units}. If the match fails, the simulation is terminated with
+an error.
+
+Here is an example of a LAMMPS script to compute the cohesive energy
+of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
+potential for Al:
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+lattice          fcc 4.032
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 26.981539
+kim_interactions Al
+run              0
+variable         Ec equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{EcJ\} eV"
+:pre
+
+The above script will end with an error in the {kim_init} line if the
+IM is changed to another potential for Al that does not work with {metal}
+units. To address this {kim_init} offers the {unit_conversion_mode}.
+If unit conversion mode {is} active, then {kim_init} calls the LAMMPS
+"units"_units.html command to set the units to the IM's required or
+preferred units. Conversion factors between the IM's units and the {user_units}
+are defined for all "physical quantities"_units.html (mass, distance, etc.).
+(Note that converting to or from the "lj" unit style is not supported.)
+These factors are stored as "internal style variables"_variable.html with
+the following standard names:
+
+_u_mass
+_u_distance
+_u_time
+_u_energy
+_u_velocity
+_u_force
+_u_torque
+_u_temperature
+_u_pressure
+_u_viscosity
+_u_charge
+_u_dipole
+_u_efield
+_u_density :pre
+
+If desired, the input script can be designed to work with these conversion
+factors so that the script will work without change with any OpenKIM IM.
+(This approach is used in the
+"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.)
+For example, the script given above for the cohesive energy of fcc Al
+can be rewritten to work with any IM regardless of units. The following
+script constructs an fcc lattice with a lattice parameter defined in
+meters, computes the total energy, and prints the cohesive energy in
+Joules regardless of the units of the IM.
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
+boundary         p p p
+lattice          fcc 4.032e-10*$\{_u_distance\}
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 4.480134e-26*$\{_u_mass\}
+kim_interactions Al
+run              0
+variable         Ec_in_J equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{Ec_in_J\} J" :pre
+
+Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert
+from SI units (specified in the {kim_init} command) to whatever units the
+IM uses (metal in this case), and the division by $\{_u_energy\}
+to convert from the IM's energy units to SI units (Joule). This script
+will work correctly for any IM for Al (KIM PM or SM) selected by the
+{kim_init} command.
+
+Care must be taken to apply unit conversion to dimensional variables read in
+from a file. For example if a configuration of atoms is read in from a
+dump file using the "read_dump"_read_dump.html command, the following can
+be done to convert the box and all atomic positions to the correct units:
+
+variable xyfinal equal xy*$\{_u_distance\}
+variable xzfinal equal xz*$\{_u_distance\}
+variable yzfinal equal yz*$\{_u_distance\}
+change_box all x scale $\{_u_distance\} &
+                       y scale $\{_u_distance\} &
+                       z scale $\{_u_distance\} &
+                       xy final $\{xyfinal\} &
+                       xz final $\{xzfinal\} &
+                       yz final $\{yzfinal\} &
+                       remap  :pre
+
+NOTE: Unit conversion will only work if the conversion factors are placed in
+all appropriate places in the input script. It is up to the user to do this
+correctly.
+
+OpenKIM IM Execution ({kim_interactions}) :h5
+
+The second and final step in using an OpenKIM IM is to execute the
+{kim_interactions} command. This command must be preceded by a {kim_init}
+command and a command that defines the number of atom types {N} (such as
+"create_box"_create_box.html).
+The {kim_interactions} command has one argument {typeargs}. This argument
+contains either a list of {N} chemical species, which defines a mapping between
+atom types in LAMMPS to the available species in the OpenKIM IM, or the
+keyword {fixed_types} for models that have a preset fixed mapping (i.e.
+the mapping between LAMMPS atom types and chemical species is defined by
+the model and cannot be changed). In the latter case, the user must consult
+the model documentation to see how many atom types there are and how they
+map to the chemical species.
+
+For example, consider an OpenKIM IM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following {kim_interactions} command would be used:
+
+kim_interactions Si Si Si C
+:pre
+
+Alternatively, for a model with a fixed mapping the command would be:
+
+kim_interactions fixed_types
+:pre
+
+The {kim_interactions} command performs all the necessary steps to set up
+the OpenKIM IM selected in the {kim_init} command. The specific actions depend
+on whether the IM is a KIM PM or a KIM SM.  For a KIM PM,
+a "pair_style kim"_pair_kim.html command is executed followed by
+the appropriate {pair_coeff} command. For example, for the
+Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
+
+kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+...  box specification lines skipped
+...
+kim_interactions Al :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
+pair_coeff * * Al  :pre
+
+For a KIM SM, the generated input commands may be more complex
+and require that LAMMPS is built with the required packages included
+for the type of potential being used. The set of commands to be executed
+is defined in the SM specification file, which is part of the SM package.
+For example, for the Strachan et al. (2003) ReaxFF SM
+set by the following commands:
+
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+...
+...  box specification lines skipped
+...
+kim_interactions C H N O  :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style reax/c lmp_control safezone 2.0 mincap 100
+pair_coeff * * ffield.reax.rdx C H N O
+fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq  :pre
+
+Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq}
+are specific to the Strachan et al. (2003) ReaxFF parameterization
+and are archived as part of the SM package in OpenKIM.
+Note also that parameters like cutoff radii and charge tolerances,
+which have an effect on IM predictions, are also included in the
+SM definition ensuring reproducibility.
+
+NOTE: When using {kim_init} and {kim_interactions} to select
+and set up an OpenKIM IM, other LAMMPS commands
+for the same functions (such as pair_style, pair_coeff, bond_style,
+bond_coeff, fixes related to charge equilibration, etc.) should normally
+not appear in the input script.
+
+Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5
+
+The {kim_query} command performs a web query to retrieve the predictions
+of the IM set by {kim_init} for material properties archived in
+"OpenKIM"_https://openkim.org.  The {kim_query} command must be preceded
+by a {kim_init} command. The result of the query is stored in a
+"string style variable"_variable.html, the name of which is given as the first
+argument of the {kim_query command}.  (For the case of multiple
+return values, the optional {split} keyword can be used after the
+variable name to separate the results into multiple variables; see
+the "example"_#split_example below.)
+The second required argument {query_function} is the name of the
+query function to be called (e.g. {get_lattice_constant_cubic}).
+All following "arguments"_Commands_parse.html are parameters handed over to
+the web query in the format {keyword=value}, where {value} is always
+an array of one or more comma-separated items in brackets.
+The list of supported keywords and the type and format of their values
+depend on the query function used. The current list of query functions
+is available on the OpenKIM webpage at
+"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query.
+
+NOTE: All query functions require the {model} keyword, which identifies
+the IM whose predictions are being queried. This keyword is automatically
+generated by {kim_query} based on the IM set in {kim_init} and must not
+be specified as an argument to {kim_query}.
+
+NOTE: Each {query_function} is associated with a default method (implemented
+as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/)
+used to compute this property. In cases where there are multiple
+methods in OpenKIM for computing a property, a {method} keyword can
+be provided to select the method of choice.  See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which methods are available for a given {query function}.
+
+{kim_query} Usage Examples and Further Clarifications: :h6
+
+The data obtained by {kim_query} commands can be used as part of the setup
+or analysis phases of LAMMPS simulations. Some examples are given below.
+
+[Define an equilibrium fcc crystal]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+lattice          fcc $\{a0\}
+... :pre
+
+The {kim_query} command retrieves from "OpenKIM"_https://openkim.org
+the equilibrium lattice constant predicted by the Ercolessi and Adams (1994)
+potential for the fcc structure and places it in
+variable {a0}. This variable is then used on the next line to set up the
+crystal. By using {kim_query}, the user is saved the trouble and possible
+error of tracking this value down, or of having to perform an energy
+minimization to find the equilibrium lattice constant.
+
+Note that in {unit_conversion_mode} the results obtained from a
+{kim_query} would need to be converted to the appropriate units system.
+For example, in the above script, the lattice command would need to be
+changed to: "lattice fcc $\{a0\}*$\{_u_distance\}".
+
+:link(split_example)
+[Define an equilibrium hcp crystal]
+
+kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
+boundary         p p p
+kim_query        latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\]
+variable         a0 equal latconst_1
+variable         c0 equal latconst_2
+variable         c_to_a equal $\{c0\}/$\{a0\}
+lattice          custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} &
+                 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75
+... :pre
+
+In this case the {kim_query} returns two arguments (since the hexagonal
+close packed (hcp) structure has two independent lattice constants).
+The default behavior of {kim_query} returns the result as a string
+with the values separated by commas. The optional keyword {split}
+separates the result values into individual variables of the form
+{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument
+and {I} ranges from 1 to the number of returned values. The number and order of
+the returned values is determined by the type of query performed.
+
+[Define a crystal at finite temperature accounting for thermal expansion]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+kim_query        alpha get_linear_thermal_expansion_coefficient_cubic  crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\]
+variable         DeltaT equal 300
+lattice          fcc $\{a0\}*$\{alpha\}*$\{DeltaT\}
+... :pre
+
+As in the previous example, the equilibrium lattice constant is obtained
+for the Ercolessi and Adams (1994) potential. However, in this case the
+crystal is scaled to the appropriate lattice constant at room temperature
+(293.15 K) by using the linear thermal expansion constant predicted by the
+potential.
+
+NOTE: When passing numerical values as arguments (as in the case
+of the temperature in the above example) it is also possible to pass a
+tolerance indicating how close to the value is considered a match.
+If no tolerance is passed a default value is used. If multiple results
+are returned (indicating that the tolerance is too large), {kim_query}
+will return an error. See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which numerical arguments and tolerances are available for a
+given {query function}.
+
+[Compute defect formation energy]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+... Build fcc crystal containing some defect and compute the total energy
+... which is stored in the variable {Etot}
+...
+kim_query        Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\]
+variable         Eform equal $\{Etot\} - count(all)*$\{Ec\}
+... :pre
+
+The defect formation energy {Eform} is computed by subtracting from {Etot} the
+ideal fcc cohesive energy of the atoms in the system obtained from
+"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential.
+
+NOTE: {kim_query} commands return results archived in
+"OpenKIM"_https://openkim.org. These results are obtained
+using programs for computing material properties
+(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM.
+In order to give credit to Test developers, the number of times results
+from these programs are queried is tracked. No other information about
+the nature of the query or its source is recorded.
+
+
+Citation of OpenKIM IMs :h4
+
+When publishing results obtained using OpenKIM IMs researchers are requested
+to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API
+"(Elliott)"_#kim-api, and the specific IM codes used in the simulations,
+in addition to the relevant scientific references for the IM.
+The citation format for an IM is displayed on its page on
+"OpenKIM"_https://openkim.org along with the corresponding BibTex file,
+and is automatically added to the LAMMPS {log.cite} file.
+
+Citing the IM software (KIM infrastructure and specific PM or SM codes)
+used in the simulation gives credit to the researchers who developed them
+and enables open source efforts like OpenKIM to function.
+
+
+[Restrictions:]
+
+The set of {kim_commands} is part of the KIM package.  It is only enabled if
+LAMMPS is built with that package. A requirement for the KIM package,
+is the KIM API library that must be downloaded from the
+"OpenKIM website"_https://openkim.org/kim-api/ and installed before
+LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed. See the KIM
+section of the "Packages details"_Packages_details.html for details.
+
+Furthermore, when using {kim_commands} to run KIM SMs, any packages required
+by the native potential being used or other commands or fixes that it invokes
+must be installed.
+
+[Related commands:]
+
+"pair_style kim"_pair_kim.html
+
+:line
+
+:link(kim-mainpaper)
+[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011).
+doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6
+
+:link(kim-api)
+[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011)
+doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A

doc/src/kim_query.txt

@@ -1,46 +0,0 @@
-"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
-
-kim_query command :h3
-
-[Syntax:]
-
-kim_query variable query_function web_query_flags :pre
-
-variable = name of a (string style) variable where the result of the query is stored
-query_function = name of the OpenKIM web API query function to be used
-web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
-
-[Examples:]
-
-kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
-  prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
-
-[Description:]
-
-The kim_query command allows to retrieve properties from the OpenKIM
-through a web query. The result is stored in a string style
-"variable"_variable.html, the name of which must be given as the first
-argument of the kim_query command.  The second required argument is the
-name of the actual query function (e.g. {get_test_result}).  All following
-arguments are parameters handed over to the web query in the format
-{keyword=value}.  The list of supported keywords and the type of how
-the value has to be encoded depends on the query function used.  This
-mirrors the functionality available on the OpenKIM webpage at
-"https://query.openkim.org"_https://query.openkim.org/
-
-[Restrictions:]
-
-This command is part of the KIM package.  It is only enabled if
-LAMMPS was built with that package.  Furthermore, its correct
-functioning depends on compiling LAMMPS with libcurl support.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_style kim"_pair_kim.html, "variable"_variable.html

doc/src/lammps.book

@@ -42,6 +42,7 @@ Commands_compute.html
 Commands_pair.html
 Commands_bond.html
 Commands_kspace.html
+Commands_removed.html
 Packages.html
 Packages_standard.html
 Packages_user.html
@@ -167,7 +168,7 @@ if.html
 include.html
 info.html
 jump.html
-kim_query.html
+kim_commands.html
 label.html
 lattice.html
 log.html
@@ -455,6 +456,7 @@ compute_global_atom.html
 compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
+compute_gyration_shape.html
 compute_heat_flux.html
 compute_hexorder_atom.html
 compute_improper.html
@@ -468,6 +470,7 @@ compute_ke_rigid.html
 compute_meso_e_atom.html
 compute_meso_rho_atom.html
 compute_meso_t_atom.html
+compute_momentum.html
 compute_msd.html
 compute_msd_chunk.html
 compute_msd_nongauss.html

doc/src/pair_adp.txt

@@ -42,16 +42,17 @@ the ADP potential files themselves.  Likewise, the ADP potential files
 list atomic masses; thus you do not need to use the "mass"_mass.html
 command to specify them.
 
-The NIST WWW site distributes and documents ADP potentials:
+[ADP potentials are available from:]
 
-http://www.ctcms.nist.gov/potentials :pre
+The NIST WWW site at http://www.ctcms.nist.gov/potentials.
+Note that ADP potentials obtained from NIST must be converted
+into the extended DYNAMO {setfl} format discussed below.
+:l
 
-Note that these must be converted into the extended DYNAMO {setfl}
+The OpenKIM Project at https://openkim.org/browse/models/by-type provides
-format discussed below.
+ADP potentials that can be used directly in LAMMPS with the "kim_commands
-
+interface"_kim_commands.html.
-The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
+:l
-who is good resource for info on interatomic potentials and file
-formats.
 
 :line
 

doc/src/pair_kim.txt

@@ -12,76 +12,72 @@ pair_style kim command :h3
 
 pair_style kim model :pre
 
-model = name of KIM model (potential)
+model = name of a KIM model (the KIM ID for models archived in OpenKIM)
 
 [Examples:]
 
-pair_style kim ex_model_Ar_P_LJ
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
-pair_coeff * * Ar Ar :pre
+pair_coeff * * Si :pre
 
 [Description:]
 
-This pair style is a wrapper on the "Knowledge Base for Interatomic
+This pair style is a wrapper on the "Open Knowledgebase of Interatomic
 Models (OpenKIM)"_https://openkim.org repository of interatomic
-potentials, so that they can be used by LAMMPS scripts.
+potentials to enable their use in LAMMPS scripts.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
+The preferred interface for using interatomic models archived in
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+OpenKIM is the "kim_commands interface"_kim_commands.html. That
-element or alloy and set of parameters, e.g. EAM for Cu with a
+interface supports both "KIM Portable Models" (PMs) that conform to the
-specific EAM potential file.
+KIM API Portable Model Interface (PMI) and can be used by any
+simulation code that conforms to the KIM API/PMI, and
+"KIM Simulator Models" that are natively implemented within a single
+simulation code (like LAMMPS) and can only be used with it.
+The {pair_style kim} command is limited to KIM PMs. It is
+used by the "kim_commands interface"_kim_commands.html as needed.
 
-See the current list of "KIM model
+NOTE: Since {pair_style kim} is called by {kim_interactions} as needed,
-drivers"_https://openkim.org/browse/model-drivers/alphabetical.
+is not recommended to be directly used in input scripts.
 
-See the current list of all "KIM
-models"_https://openkim.org/browse/models/by-model-drivers
-
-To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org.  The KIM
-section of the "Packages details"_Packages_details.html doc page has
-instructions on how to do this with a simple make command, when
-building LAMMPS.
-
-See the examples/kim dir for an input script that uses a KIM model
-(potential) for Lennard-Jones.
- 
 :line
 
-The argument {model} is the name of the KIM model for a specific
+The argument {model} is the name of the KIM PM.
-potential as KIM defines it.  In principle, LAMMPS can invoke any KIM
+For potentials archived in OpenKIM
-model.  You should get an error or warning message from either LAMMPS
+this is the extended KIM ID (see "kim_commands"_kim_commands.html
-or KIM if there is an incompatibility.
+for details). LAMMPS can invoke any KIM PM, however there can
+be incompatibilities (for example due to unit matching issues).
+In the event of an incompatibility, the code will terminate with
+an error message. Check both the LAMMPS and KIM log files for details.
 
-Only a single pair_coeff command is used with the {kim} style which
+Only a single {pair_coeff} command is used with the {kim} style, which
-specifies the mapping of LAMMPS atom types to KIM elements.  This is
+specifies the mapping of LAMMPS atom types to the species supported by
-done by specifying N additional arguments after the * * in the
+the KIM PM.  This is done by specifying {N} additional arguments
-pair_coeff command, where N is the number of LAMMPS atom types:
+after the * * in the {pair_coeff} command, where {N} is the number of
+LAMMPS atom types:
 
 N element names = mapping of KIM elements to atom types :ul
 
-As an example, imagine the KIM model supports Si and C atoms.  If your
+For example, consider a KIM PM that supports Si and C species.
-LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
+If the LAMMPS simulation has four atom types, where the first three are Si,
-and the 4th to be C, you would use the following pair_coeff command:
+and the fourth is C, the following {pair_coeff} command would be used:
 
 pair_coeff * * Si Si Si C :pre
 
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first two arguments must be * * so as to span all LAMMPS atom types.
-The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
+The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as
-defined within KIM.  The final C argument maps LAMMPS atom type 4 to C
+defined within KIM PM.  The final C argument maps LAMMPS atom type 4 to C.
-as defined within KIM.
 
 :line
 
 In addition to the usual LAMMPS error messages, the KIM library itself
 may generate errors, which should be printed to the screen.  In this
-case it is also useful to check the kim.log file for additional error
+case it is also useful to check the {kim.log} file for additional error
-information.  The file kim.log should be generated in the same
+information.  The file {kim.log} should be generated in the same
 directory where LAMMPS is running.
 
 To download, build, and install the KIM library on your system, see
-the lib/kim/README file.  Once you have done this and built LAMMPS
+the {lib/kim/README} file.  Once you have done this and built LAMMPS
 with the KIM package installed you can run the example input scripts
-in examples/kim.
+in {examples/kim}.
 
 :line
 
@@ -103,15 +99,14 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This pair style is part of the KIM package.  It is only enabled if
+This pair style is part of the KIM package. See details on
-LAMMPS was built with that package.  See the "Build
+restrictions in "kim_commands"_kim_commands.html.
-package"_Build_package.html doc page for more info.
 
 This current version of pair_style kim is compatible with the
 kim-api package version 2.0.0 and higher.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html
 
 [Default:] none

doc/utils/sphinx-config/false_positives.txt

@@ -20,6 +20,7 @@ acolor
 acos
 Acta
 actinide
+acylindricity
 addforce
 Addington
 addtorque
@@ -113,6 +114,7 @@ askoose
 asphere
 ASPHERE
 aspherical
+asphericity
 Asq
 assignee
 Asta
@@ -481,6 +483,7 @@ cvff
 cwiggle
 cygwin
 Cygwin
+cylindrically
 Cyrot
 cyrstals
 Daivis
@@ -526,6 +529,7 @@ decrementing
 deeppink
 deepskyblue
 defgrad
+defn
 deformable
 del
 deleteIDs
@@ -574,6 +578,7 @@ Dihedrals
 dihydride
 Dij
 dimdim
+dimensioned
 dimensionality
 dimgray
 dipolar
@@ -603,6 +608,7 @@ Dobson
 Dodds
 dodgerblue
 dof
+doi
 Donadio
 dotc
 Doty
@@ -754,6 +760,7 @@ equilibrating
 equilibration
 Equilibria
 equilization
+Ercolessi
 eradius
 erate
 erc
@@ -880,6 +887,7 @@ Fogarty
 Foiles
 fopenmp
 forestgreen
+formatarg
 formulae
 Forschungszentrum
 Fortran
@@ -1514,6 +1522,7 @@ lz
 Maaravi
 Mackay
 Mackrodt
+Macromolecules
 macroparticle
 Madura
 Magda
@@ -1539,6 +1548,7 @@ Mandelli
 Manh
 manifoldforce
 Manolopoulos
+manpages
 manybody
 MANYBODY
 Maras
@@ -1619,6 +1629,7 @@ meso
 mesoparticle
 mesoscale
 mesoscopic
+metadata
 metadynamics
 Metadynamics
 Methfessel
@@ -2257,6 +2268,7 @@ quati
 quatj
 quatk
 quatw
+queryargs
 Queteschiner
 qw
 qx
@@ -2286,6 +2298,7 @@ rcutfac
 rdc
 rdf
 RDideal
+rdx
 README
 realtime
 reamin
@@ -2312,6 +2325,8 @@ Rensselaer
 reparameterizing
 repo
 representable
+Reproducibility
+reproducibility
 repuls
 rescale
 rescaled
@@ -2602,6 +2617,7 @@ Stoll
 stopstep
 Stouch
 Straatsma
+Strachan
 Stratford
 Strathclyde
 Straub
@@ -2629,6 +2645,7 @@ superset
 supersphere
 Supinski
 surfactants
+Suter
 Sutmann
 svn
 sw
@@ -2690,6 +2707,7 @@ th
 Thakkar
 thb
 thei
+Theodorou
 Theor
 thermalization
 thermalize
@@ -2812,6 +2830,7 @@ txt
 typeI
 typeJ
 typeN
+typeargs
 Tz
 Tzou
 ub
@@ -2840,6 +2859,7 @@ undump
 uniaxial
 uniaxially
 unimodal
+unitarg
 unitless
 Universite
 unix

examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized

@@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
 fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
 
 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized

@@ -0,0 +1,48 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization no &
+  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+fix 1 all nve/limit .03
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 1000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1

@@ -1,370 +0,0 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-read_data tiny_nylon.data
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  44 impropers
-  4 = max # of 1-2 neighbors
-  6 = max # of 1-3 neighbors
-  12 = max # of 1-4 neighbors
-  41 = max # of special neighbors
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.data_template
-Read molecule mol1:
-  18 atoms with max type 8
-  16 bonds with max type 14
-  25 angles with max type 28
-  23 dihedrals with max type 36
-  14 impropers with max type 11
-molecule mol2 rxn1_stp1_reacted.data_template
-Read molecule mol2:
-  18 atoms with max type 9
-  17 bonds with max type 13
-  31 angles with max type 27
-  39 dihedrals with max type 33
-  20 impropers with max type 1
-molecule mol3 rxn1_stp2_unreacted.data_template
-Read molecule mol3:
-  15 atoms with max type 9
-  14 bonds with max type 13
-  25 angles with max type 27
-  30 dihedrals with max type 33
-  16 impropers with max type 1
-molecule mol4 rxn1_stp2_reacted.data_template
-Read molecule mol4:
-  15 atoms with max type 11
-  13 bonds with max type 15
-  19 angles with max type 29
-  16 dihedrals with max type 32
-  10 impropers with max type 13
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
-WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-
-fix 1 statted_grp nvt temp 300 300 100
-
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
-
-# restart 100 restart1 restart2
-
-run 10000
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.0534597
-  grid = 2 2 2
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0402256
-  estimated relative force accuracy = 0.000121138
-  using double precision FFTs
-  3d grid and FFT values/proc = 343 8
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-WARNING: Inconsistent image flags (../domain.cpp:786)
-Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
-Step Temp Press Density f_myrxns[1] f_myrxns[2] 
-       0          300    346.78165 0.0034851739            0            0 
-      50    296.70408    -51.30066 0.0034851739            1            0 
-     100    274.25324    46.715512 0.0034851739            1            1 
-     150    471.61579    31.321598 0.0034851739            1            1 
-     200    362.87766    42.061118 0.0034851739            1            1 
-     250    367.58058    65.303109 0.0034851739            1            1 
-     300    372.38236   -52.421725 0.0034851739            1            1 
-     350    297.69957    17.869945 0.0034851739            1            1 
-     400    258.30433     49.19156 0.0034851739            1            1 
-     450    253.34384   -5.8162637 0.0034851739            1            1 
-     500    269.96465   -43.337517 0.0034851739            1            1 
-     550    303.23718    10.180246 0.0034851739            1            1 
-     600    329.59579    -48.97461 0.0034851739            1            1 
-     650    350.42568    50.983183 0.0034851739            1            1 
-     700    342.03272     35.43465 0.0034851739            1            1 
-     750    269.23405   -41.873166 0.0034851739            1            1 
-     800    245.15025    13.953092 0.0034851739            1            1 
-     850    257.85421   -3.1492141 0.0034851739            1            1 
-     900    316.15644    7.7798301 0.0034851739            1            1 
-     950     299.9124    -15.77014 0.0034851739            1            1 
-    1000    302.89968   -17.049693 0.0034851739            1            1 
-    1050    308.91651     71.84632 0.0034851739            1            1 
-    1100    348.43932   -18.742012 0.0034851739            1            1 
-    1150    309.03036    50.536311 0.0034851739            1            1 
-    1200     318.9761   -16.905746 0.0034851739            1            1 
-    1250    320.42806 -0.057975092 0.0034851739            1            1 
-    1300     289.7824    18.200772 0.0034851739            1            1 
-    1350    284.79836   -9.1978427 0.0034851739            1            1 
-    1400    325.43292    42.082833 0.0034851739            1            1 
-    1450     261.5041   -37.823325 0.0034851739            1            1 
-    1500    298.88723   -5.1647385 0.0034851739            1            1 
-    1550    291.37403   -7.7764201 0.0034851739            1            1 
-    1600    293.83475      22.2458 0.0034851739            1            1 
-    1650    293.80611    24.202512 0.0034851739            1            1 
-    1700    291.70205   -23.397884 0.0034851739            1            1 
-    1750    292.32437   -10.671214 0.0034851739            1            1 
-    1800    302.01367   -11.671025 0.0034851739            1            1 
-    1850     322.1651    24.438331 0.0034851739            1            1 
-    1900    310.45076    45.343592 0.0034851739            1            1 
-    1950    325.91745   -19.847809 0.0034851739            1            1 
-    2000    276.89662    63.387098 0.0034851739            1            1 
-    2050    311.33783   -24.683247 0.0034851739            1            1 
-    2100     346.2336   -27.526891 0.0034851739            1            1 
-    2150    345.30604   -15.722411 0.0034851739            1            1 
-    2200     346.7718   -17.857633 0.0034851739            1            1 
-    2250    304.28676   -1.9965581 0.0034851739            1            1 
-    2300    322.56372   -31.786868 0.0034851739            1            1 
-    2350    282.64326    6.1982735 0.0034851739            1            1 
-    2400    286.65759   -63.207781 0.0034851739            1            1 
-    2450    257.05528    32.931491 0.0034851739            1            1 
-    2500    283.64386    26.912373 0.0034851739            1            1 
-    2550    299.54005    27.277039 0.0034851739            1            1 
-    2600    283.92503    14.660972 0.0034851739            1            1 
-    2650    321.93453   -18.977358 0.0034851739            1            1 
-    2700     376.7189    31.826935 0.0034851739            1            1 
-    2750    372.20075   -32.821697 0.0034851739            1            1 
-    2800    361.40604    83.035183 0.0034851739            1            1 
-    2850    332.27269   -23.927452 0.0034851739            1            1 
-    2900    331.14638  -0.12328446 0.0034851739            1            1 
-    2950    303.67489   -24.078857 0.0034851739            1            1 
-    3000    311.40462    21.563537 0.0034851739            1            1 
-    3050    284.72849   -23.849667 0.0034851739            1            1 
-    3100    303.48477    39.347763 0.0034851739            1            1 
-    3150     264.2739  -0.22299879 0.0034851739            1            1 
-    3200    300.03351    31.545323 0.0034851739            1            1 
-    3250    288.56663    5.7225228 0.0034851739            1            1 
-    3300    200.13238   -31.239655 0.0034851739            1            1 
-    3350    231.32512    16.631728 0.0034851739            1            1 
-    3400    260.57402    2.1717992 0.0034851739            1            1 
-    3450    301.47128   -42.210623 0.0034851739            1            1 
-    3500    321.77414    40.074365 0.0034851739            1            1 
-    3550    353.21858    28.387783 0.0034851739            1            1 
-    3600    331.45989   -57.800858 0.0034851739            1            1 
-    3650    303.88123     44.86596 0.0034851739            1            1 
-    3700    329.73833  -0.80615652 0.0034851739            1            1 
-    3750    297.55588  -0.49626039 0.0034851739            1            1 
-    3800    286.38794   -10.010003 0.0034851739            1            1 
-    3850    290.17417    -43.51187 0.0034851739            1            1 
-    3900    247.88933     51.23735 0.0034851739            1            1 
-    3950    332.31324   -18.194985 0.0034851739            1            1 
-    4000    325.56802    18.402825 0.0034851739            1            1 
-    4050    338.37593    36.430977 0.0034851739            1            1 
-    4100    370.95478    39.290285 0.0034851739            1            1 
-    4150    348.47859   -7.0779678 0.0034851739            1            1 
-    4200    241.30632   -33.371788 0.0034851739            1            1 
-    4250    242.17258    -9.986197 0.0034851739            1            1 
-    4300    300.85311   -7.9244294 0.0034851739            1            1 
-    4350    273.15684   -21.257283 0.0034851739            1            1 
-    4400    305.77463   -5.8720722 0.0034851739            1            1 
-    4450    314.97697      45.0373 0.0034851739            1            1 
-    4500    310.77723    16.958773 0.0034851739            1            1 
-    4550     302.1742    12.156862 0.0034851739            1            1 
-    4600    319.74799      6.84889 0.0034851739            1            1 
-    4650    270.86805   -13.767905 0.0034851739            1            1 
-    4700    249.81731   -31.197487 0.0034851739            1            1 
-    4750    285.86481   -9.8916364 0.0034851739            1            1 
-    4800    233.98321    7.1338571 0.0034851739            1            1 
-    4850    302.60551    49.262889 0.0034851739            1            1 
-    4900    316.55056    34.663247 0.0034851739            1            1 
-    4950    357.32741    11.583006 0.0034851739            1            1 
-    5000    400.21045   -8.1781061 0.0034851739            1            1 
-    5050    390.01845   -20.490275 0.0034851739            1            1 
-    5100    378.84247   -41.328757 0.0034851739            1            1 
-    5150    324.02038   -15.023862 0.0034851739            1            1 
-    5200    262.08429    10.937354 0.0034851739            1            1 
-    5250    255.75508    16.381455 0.0034851739            1            1 
-    5300    277.84989     40.68232 0.0034851739            1            1 
-    5350    302.92832    9.1989494 0.0034851739            1            1 
-    5400     283.7196   -1.6584671 0.0034851739            1            1 
-    5450    300.71266   -4.7030295 0.0034851739            1            1 
-    5500     343.5499  -0.30550044 0.0034851739            1            1 
-    5550    369.51271    21.691649 0.0034851739            1            1 
-    5600    372.69789    -38.67994 0.0034851739            1            1 
-    5650    327.41266    11.352137 0.0034851739            1            1 
-    5700    278.98614   -23.827304 0.0034851739            1            1 
-    5750    308.30054   -20.756187 0.0034851739            1            1 
-    5800    341.45594    28.058441 0.0034851739            1            1 
-    5850    322.97844   -10.731921 0.0034851739            1            1 
-    5900    304.53591    32.825279 0.0034851739            1            1 
-    5950     287.1752   -36.780091 0.0034851739            1            1 
-    6000    296.52681    18.781896 0.0034851739            1            1 
-    6050    314.25442    15.992829 0.0034851739            1            1 
-    6100    313.86576    3.4342714 0.0034851739            1            1 
-    6150    325.64196    32.392039 0.0034851739            1            1 
-    6200    367.42931   -27.160706 0.0034851739            1            1 
-    6250    369.30798    39.020934 0.0034851739            1            1 
-    6300    328.92285   -23.175157 0.0034851739            1            1 
-    6350    305.63077    4.9024453 0.0034851739            1            1 
-    6400    241.70341   -13.676629 0.0034851739            1            1 
-    6450    265.66717      2.40612 0.0034851739            1            1 
-    6500    249.36037    13.420255 0.0034851739            1            1 
-    6550    294.53814    10.853462 0.0034851739            1            1 
-    6600     308.2025    18.995308 0.0034851739            1            1 
-    6650    305.43797    -49.56785 0.0034851739            1            1 
-    6700    320.27344    11.336281 0.0034851739            1            1 
-    6750    321.78666   -23.463899 0.0034851739            1            1 
-    6800    303.40388    7.6224553 0.0034851739            1            1 
-    6850    297.18966     51.52256 0.0034851739            1            1 
-    6900    284.18909   -8.4947203 0.0034851739            1            1 
-    6950    331.03663    13.233655 0.0034851739            1            1 
-    7000    311.37928   -43.265479 0.0034851739            1            1 
-    7050    286.81661   -14.174683 0.0034851739            1            1 
-    7100    302.84119    12.048954 0.0034851739            1            1 
-    7150    297.19357   -43.111968 0.0034851739            1            1 
-    7200    332.47359    26.048249 0.0034851739            1            1 
-    7250    262.70677    41.176242 0.0034851739            1            1 
-    7300    250.61405   -23.413982 0.0034851739            1            1 
-    7350    296.91117     35.88133 0.0034851739            1            1 
-    7400    245.09229   -13.447194 0.0034851739            1            1 
-    7450    272.28131   -23.322585 0.0034851739            1            1 
-    7500    209.04985    13.871239 0.0034851739            1            1 
-    7550    255.00955    4.9325621 0.0034851739            1            1 
-    7600    312.30937   -37.368274 0.0034851739            1            1 
-    7650    305.65903    55.245496 0.0034851739            1            1 
-    7700    325.09504   -18.347711 0.0034851739            1            1 
-    7750    363.28282   -22.479686 0.0034851739            1            1 
-    7800    350.17429    26.849547 0.0034851739            1            1 
-    7850    271.70853   -17.764575 0.0034851739            1            1 
-    7900    272.66484   -11.701967 0.0034851739            1            1 
-    7950    298.60202   -12.765675 0.0034851739            1            1 
-    8000    274.58852    49.641532 0.0034851739            1            1 
-    8050    304.72347  -0.55414183 0.0034851739            1            1 
-    8100    328.30757   -39.861301 0.0034851739            1            1 
-    8150    406.67601    2.8999409 0.0034851739            1            1 
-    8200    332.20083   -51.217399 0.0034851739            1            1 
-    8250    354.50609    53.128769 0.0034851739            1            1 
-    8300     337.2758     20.68562 0.0034851739            1            1 
-    8350    361.89708   -54.185869 0.0034851739            1            1 
-    8400    305.63496    24.058529 0.0034851739            1            1 
-    8450    303.27461     4.304683 0.0034851739            1            1 
-    8500    253.53694   -10.909021 0.0034851739            1            1 
-    8550    277.03017    23.241479 0.0034851739            1            1 
-    8600    291.41844   -22.240665 0.0034851739            1            1 
-    8650    307.85368    31.919587 0.0034851739            1            1 
-    8700    309.19724   0.53529642 0.0034851739            1            1 
-    8750     354.6583    11.565515 0.0034851739            1            1 
-    8800    329.78598      19.5996 0.0034851739            1            1 
-    8850    240.79198    21.803515 0.0034851739            1            1 
-    8900    318.40749   -59.816923 0.0034851739            1            1 
-    8950    308.47211   -57.808635 0.0034851739            1            1 
-    9000    271.51207    50.943482 0.0034851739            1            1 
-    9050     249.4005    6.7529187 0.0034851739            1            1 
-    9100     221.8772    47.196092 0.0034851739            1            1 
-    9150     297.9351    4.0058184 0.0034851739            1            1 
-    9200    274.85051   -24.774393 0.0034851739            1            1 
-    9250    336.04757    5.3799028 0.0034851739            1            1 
-    9300    380.44956   -22.389381 0.0034851739            1            1 
-    9350     336.9824    23.050616 0.0034851739            1            1 
-    9400    304.46425    32.530218 0.0034851739            1            1 
-    9450    317.55591   -22.265425 0.0034851739            1            1 
-    9500    323.70901   -7.0159787 0.0034851739            1            1 
-    9550    316.07308    28.062131 0.0034851739            1            1 
-    9600    262.74608  -0.78519192 0.0034851739            1            1 
-    9650    271.55045   -21.430123 0.0034851739            1            1 
-    9700     239.6022    14.483637 0.0034851739            1            1 
-    9750     338.1437  -0.72765302 0.0034851739            1            1 
-    9800    334.50189    19.495144 0.0034851739            1            1 
-    9850    354.87554    19.272719 0.0034851739            1            1 
-    9900    334.02141   -22.393457 0.0034851739            1            1 
-    9950    293.63651    19.178873 0.0034851739            1            1 
-   10000    319.81736    21.904414 0.0034851739            1            1 
-Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
-
-Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.26152    | 0.26152    | 0.26152    |   0.0 | 14.14
-Bond    | 0.74069    | 0.74069    | 0.74069    |   0.0 | 40.04
-Kspace  | 0.30505    | 0.30505    | 0.30505    |   0.0 | 16.49
-Neigh   | 0.39991    | 0.39991    | 0.39991    |   0.0 | 21.62
-Comm    | 0.02261    | 0.02261    | 0.02261    |   0.0 |  1.22
-Output  | 0.0034585  | 0.0034585  | 0.0034585  |   0.0 |  0.19
-Modify  | 0.099979   | 0.099979   | 0.099979   |   0.0 |  5.40
-Other   |            | 0.01666    |            |       |  0.90
-
-Nlocal:    44 ave 44 max 44 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    44 ave 44 max 44 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    823 ave 823 max 823 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 823
-Ave neighs/atom = 18.7045
-Ave special neighs/atom = 9.77273
-Neighbor list builds = 10000
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01

examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4

@@ -1,370 +0,0 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-read_data tiny_nylon.data
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  44 impropers
-  4 = max # of 1-2 neighbors
-  6 = max # of 1-3 neighbors
-  12 = max # of 1-4 neighbors
-  41 = max # of special neighbors
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.data_template
-Read molecule mol1:
-  18 atoms with max type 8
-  16 bonds with max type 14
-  25 angles with max type 28
-  23 dihedrals with max type 36
-  14 impropers with max type 11
-molecule mol2 rxn1_stp1_reacted.data_template
-Read molecule mol2:
-  18 atoms with max type 9
-  17 bonds with max type 13
-  31 angles with max type 27
-  39 dihedrals with max type 33
-  20 impropers with max type 1
-molecule mol3 rxn1_stp2_unreacted.data_template
-Read molecule mol3:
-  15 atoms with max type 9
-  14 bonds with max type 13
-  25 angles with max type 27
-  30 dihedrals with max type 33
-  16 impropers with max type 1
-molecule mol4 rxn1_stp2_reacted.data_template
-Read molecule mol4:
-  15 atoms with max type 11
-  13 bonds with max type 15
-  19 angles with max type 29
-  16 dihedrals with max type 32
-  10 impropers with max type 13
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
-WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-
-fix 1 statted_grp nvt temp 300 300 100
-
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
-
-# restart 100 restart1 restart2
-
-run 10000
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.0534597
-  grid = 2 2 2
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0402256
-  estimated relative force accuracy = 0.000121138
-  using double precision FFTs
-  3d grid and FFT values/proc = 252 2
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-WARNING: Inconsistent image flags (../domain.cpp:786)
-Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
-Step Temp Press Density f_myrxns[1] f_myrxns[2] 
-       0          300    346.78165 0.0034851739            0            0 
-      50    296.70408    -51.30066 0.0034851739            1            0 
-     100    274.25324    46.715512 0.0034851739            1            1 
-     150    471.61579    31.321598 0.0034851739            1            1 
-     200    362.87766    42.061118 0.0034851739            1            1 
-     250    367.58058    65.303109 0.0034851739            1            1 
-     300    372.38236   -52.421725 0.0034851739            1            1 
-     350    297.69957    17.869945 0.0034851739            1            1 
-     400    258.30433     49.19156 0.0034851739            1            1 
-     450    253.34384   -5.8162637 0.0034851739            1            1 
-     500    269.96465   -43.337517 0.0034851739            1            1 
-     550    303.23718    10.180246 0.0034851739            1            1 
-     600    329.59579    -48.97461 0.0034851739            1            1 
-     650    350.42568    50.983183 0.0034851739            1            1 
-     700    342.03272     35.43465 0.0034851739            1            1 
-     750    269.23405   -41.873166 0.0034851739            1            1 
-     800    245.15025    13.953092 0.0034851739            1            1 
-     850    257.85421   -3.1492141 0.0034851739            1            1 
-     900    316.15644    7.7798301 0.0034851739            1            1 
-     950     299.9124    -15.77014 0.0034851739            1            1 
-    1000    302.89968   -17.049693 0.0034851739            1            1 
-    1050    308.91651     71.84632 0.0034851739            1            1 
-    1100    348.43932   -18.742012 0.0034851739            1            1 
-    1150    309.03036    50.536311 0.0034851739            1            1 
-    1200     318.9761   -16.905746 0.0034851739            1            1 
-    1250    320.42806 -0.057975092 0.0034851739            1            1 
-    1300     289.7824    18.200772 0.0034851739            1            1 
-    1350    284.79836   -9.1978427 0.0034851739            1            1 
-    1400    325.43292    42.082833 0.0034851739            1            1 
-    1450     261.5041   -37.823325 0.0034851739            1            1 
-    1500    298.88723   -5.1647385 0.0034851739            1            1 
-    1550    291.37403   -7.7764201 0.0034851739            1            1 
-    1600    293.83475      22.2458 0.0034851739            1            1 
-    1650    293.80611    24.202512 0.0034851739            1            1 
-    1700    291.70205   -23.397884 0.0034851739            1            1 
-    1750    292.32437   -10.671214 0.0034851739            1            1 
-    1800    302.01367   -11.671025 0.0034851739            1            1 
-    1850     322.1651    24.438331 0.0034851739            1            1 
-    1900    310.45076    45.343592 0.0034851739            1            1 
-    1950    325.91745   -19.847809 0.0034851739            1            1 
-    2000    276.89662    63.387098 0.0034851739            1            1 
-    2050    311.33783   -24.683247 0.0034851739            1            1 
-    2100     346.2336   -27.526891 0.0034851739            1            1 
-    2150    345.30604   -15.722411 0.0034851739            1            1 
-    2200     346.7718   -17.857633 0.0034851739            1            1 
-    2250    304.28676   -1.9965581 0.0034851739            1            1 
-    2300    322.56372   -31.786868 0.0034851739            1            1 
-    2350    282.64326    6.1982735 0.0034851739            1            1 
-    2400    286.65759   -63.207781 0.0034851739            1            1 
-    2450    257.05528    32.931491 0.0034851739            1            1 
-    2500    283.64386    26.912373 0.0034851739            1            1 
-    2550    299.54005    27.277039 0.0034851739            1            1 
-    2600    283.92503    14.660972 0.0034851739            1            1 
-    2650    321.93453   -18.977358 0.0034851739            1            1 
-    2700     376.7189    31.826935 0.0034851739            1            1 
-    2750    372.20075   -32.821697 0.0034851739            1            1 
-    2800    361.40604    83.035183 0.0034851739            1            1 
-    2850    332.27269   -23.927452 0.0034851739            1            1 
-    2900    331.14638  -0.12328446 0.0034851739            1            1 
-    2950    303.67489   -24.078857 0.0034851739            1            1 
-    3000    311.40462    21.563537 0.0034851739            1            1 
-    3050    284.72849   -23.849667 0.0034851739            1            1 
-    3100    303.48477    39.347763 0.0034851739            1            1 
-    3150     264.2739  -0.22299878 0.0034851739            1            1 
-    3200    300.03351    31.545323 0.0034851739            1            1 
-    3250    288.56663    5.7225229 0.0034851739            1            1 
-    3300    200.13238   -31.239655 0.0034851739            1            1 
-    3350    231.32512    16.631728 0.0034851739            1            1 
-    3400    260.57402    2.1717992 0.0034851739            1            1 
-    3450    301.47128   -42.210623 0.0034851739            1            1 
-    3500    321.77414    40.074365 0.0034851739            1            1 
-    3550    353.21858    28.387783 0.0034851739            1            1 
-    3600    331.45989   -57.800858 0.0034851739            1            1 
-    3650    303.88123     44.86596 0.0034851739            1            1 
-    3700    329.73833   -0.8061567 0.0034851739            1            1 
-    3750    297.55588  -0.49626022 0.0034851739            1            1 
-    3800    286.38794   -10.010003 0.0034851739            1            1 
-    3850    290.17417    -43.51187 0.0034851739            1            1 
-    3900    247.88933     51.23735 0.0034851739            1            1 
-    3950    332.31324   -18.194985 0.0034851739            1            1 
-    4000    325.56802    18.402825 0.0034851739            1            1 
-    4050    338.37594    36.430977 0.0034851739            1            1 
-    4100    370.95478    39.290285 0.0034851739            1            1 
-    4150    348.47859   -7.0779683 0.0034851739            1            1 
-    4200    241.30632   -33.371789 0.0034851739            1            1 
-    4250    242.17258   -9.9861962 0.0034851739            1            1 
-    4300    300.85311    -7.924429 0.0034851739            1            1 
-    4350    273.15684   -21.257282 0.0034851739            1            1 
-    4400    305.77464   -5.8720712 0.0034851739            1            1 
-    4450    314.97697    45.037299 0.0034851739            1            1 
-    4500    310.77723    16.958771 0.0034851739            1            1 
-    4550    302.17421    12.156862 0.0034851739            1            1 
-    4600    319.74799    6.8488914 0.0034851739            1            1 
-    4650    270.86805   -13.767907 0.0034851739            1            1 
-    4700    249.81731   -31.197484 0.0034851739            1            1 
-    4750    285.86481   -9.8916332 0.0034851739            1            1 
-    4800    233.98321    7.1338518 0.0034851739            1            1 
-    4850    302.60551    49.262886 0.0034851739            1            1 
-    4900    316.55055    34.663238 0.0034851739            1            1 
-    4950    357.32741    11.583013 0.0034851739            1            1 
-    5000    400.21044   -8.1780861 0.0034851739            1            1 
-    5050    390.01845   -20.490268 0.0034851739            1            1 
-    5100    378.84249   -41.328772 0.0034851739            1            1 
-    5150    324.02039   -15.023852 0.0034851739            1            1 
-    5200    262.08427    10.937367 0.0034851739            1            1 
-    5250    255.75506    16.381495 0.0034851739            1            1 
-    5300    277.84991    40.682283 0.0034851739            1            1 
-    5350    302.92834    9.1989644 0.0034851739            1            1 
-    5400    283.71964   -1.6583895 0.0034851739            1            1 
-    5450    300.71261    -4.703054 0.0034851739            1            1 
-    5500    343.54987  -0.30546396 0.0034851739            1            1 
-    5550    369.51272    21.691639 0.0034851739            1            1 
-    5600    372.69786   -38.679919 0.0034851739            1            1 
-    5650    327.41256    11.352201 0.0034851739            1            1 
-    5700     278.9861    -23.82728 0.0034851739            1            1 
-    5750    308.30037   -20.756238 0.0034851739            1            1 
-    5800     341.4559    28.058314 0.0034851739            1            1 
-    5850     322.9786   -10.731862 0.0034851739            1            1 
-    5900    304.53598    32.825105 0.0034851739            1            1 
-    5950    287.17515   -36.780057 0.0034851739            1            1 
-    6000    296.52688    18.782156 0.0034851739            1            1 
-    6050    314.25411     15.99272 0.0034851739            1            1 
-    6100    313.86572    3.4344108 0.0034851739            1            1 
-    6150    325.64197     32.39212 0.0034851739            1            1 
-    6200     367.4298   -27.161154 0.0034851739            1            1 
-    6250    369.30937    39.020881 0.0034851739            1            1 
-    6300    328.92245   -23.175612 0.0034851739            1            1 
-    6350     305.6293    4.9011587 0.0034851739            1            1 
-    6400    241.70456   -13.675247 0.0034851739            1            1 
-    6450    265.66574    2.4049735 0.0034851739            1            1 
-    6500     249.3592    13.420453 0.0034851739            1            1 
-    6550     294.5367    10.856753 0.0034851739            1            1 
-    6600    308.20246    18.992923 0.0034851739            1            1 
-    6650    305.43756    -49.57151 0.0034851739            1            1 
-    6700    320.27395    11.339101 0.0034851739            1            1 
-    6750     321.7875   -23.463361 0.0034851739            1            1 
-    6800    303.40316    7.6256997 0.0034851739            1            1 
-    6850    297.18652     51.52186 0.0034851739            1            1 
-    6900    284.19084    -8.496294 0.0034851739            1            1 
-    6950    331.04173    13.227745 0.0034851739            1            1 
-    7000    311.38027    -43.26105 0.0034851739            1            1 
-    7050    286.82046   -14.171194 0.0034851739            1            1 
-    7100    302.81691    12.058085 0.0034851739            1            1 
-    7150    297.18018   -43.110658 0.0034851739            1            1 
-    7200    332.46131    26.051496 0.0034851739            1            1 
-    7250    262.72288    41.161451 0.0034851739            1            1 
-    7300    250.62739   -23.440907 0.0034851739            1            1 
-    7350    296.92141    35.869216 0.0034851739            1            1 
-    7400    245.06807   -13.467896 0.0034851739            1            1 
-    7450     272.2659   -23.292836 0.0034851739            1            1 
-    7500    209.05776    13.888665 0.0034851739            1            1 
-    7550    255.03716    4.9662624 0.0034851739            1            1 
-    7600    312.26011   -37.350427 0.0034851739            1            1 
-    7650     305.5823    55.208039 0.0034851739            1            1 
-    7700    325.13382   -18.370791 0.0034851739            1            1 
-    7750    363.24898   -22.473126 0.0034851739            1            1 
-    7800    350.19254    26.792307 0.0034851739            1            1 
-    7850    271.76418   -17.843445 0.0034851739            1            1 
-    7900    272.70301   -11.709349 0.0034851739            1            1 
-    7950     298.5993   -12.736235 0.0034851739            1            1 
-    8000    274.52611    49.657345 0.0034851739            1            1 
-    8050    304.73711  -0.52485689 0.0034851739            1            1 
-    8100    328.29239   -39.901891 0.0034851739            1            1 
-    8150    406.52096    2.8669076 0.0034851739            1            1 
-    8200    332.17309   -51.168754 0.0034851739            1            1 
-    8250    354.68419    53.003157 0.0034851739            1            1 
-    8300    337.28934    20.766408 0.0034851739            1            1 
-    8350    361.81133   -54.159227 0.0034851739            1            1 
-    8400    305.59597    24.011667 0.0034851739            1            1 
-    8450    303.25823     4.423341 0.0034851739            1            1 
-    8500    253.50747   -11.026949 0.0034851739            1            1 
-    8550    277.13504    23.204625 0.0034851739            1            1 
-    8600    291.40211   -22.253861 0.0034851739            1            1 
-    8650    307.93765     32.14162 0.0034851739            1            1 
-    8700     309.1529   0.36279434 0.0034851739            1            1 
-    8750    355.10326    11.677219 0.0034851739            1            1 
-    8800    330.21328    19.235269 0.0034851739            1            1 
-    8850    241.29109    21.707386 0.0034851739            1            1 
-    8900    319.15363   -60.010115 0.0034851739            1            1 
-    8950    308.88552   -57.637014 0.0034851739            1            1 
-    9000    272.22373     51.15837 0.0034851739            1            1 
-    9050    248.84947    7.3390565 0.0034851739            1            1 
-    9100    221.91564    48.387079 0.0034851739            1            1 
-    9150    298.03506    2.9058639 0.0034851739            1            1 
-    9200    274.25114   -24.597819 0.0034851739            1            1 
-    9250    334.08373    5.1079577 0.0034851739            1            1 
-    9300    383.07285   -23.274763 0.0034851739            1            1 
-    9350    335.00581     20.94212 0.0034851739            1            1 
-    9400    309.23862    34.074744 0.0034851739            1            1 
-    9450    312.62262   -28.468057 0.0034851739            1            1 
-    9500    324.54274     2.851136 0.0034851739            1            1 
-    9550    313.32781    22.468182 0.0034851739            1            1 
-    9600    269.04372     4.064934 0.0034851739            1            1 
-    9650    270.98476   -21.520127 0.0034851739            1            1 
-    9700     236.8736    16.250728 0.0034851739            1            1 
-    9750    333.94686    1.6864148 0.0034851739            1            1 
-    9800    330.91875    12.150018 0.0034851739            1            1 
-    9850     343.8603    25.338853 0.0034851739            1            1 
-    9900    330.93364   -28.292992 0.0034851739            1            1 
-    9950    291.25518    25.795948 0.0034851739            1            1 
-   10000    319.25565    25.323846 0.0034851739            1            1 
-Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
-
-Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
-93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0030422  | 0.10454    | 0.35211    |  44.8 |  2.94
-Bond    | 0.0063896  | 0.29222    | 0.94356    |  71.3 |  8.22
-Kspace  | 0.88508    | 1.6486     | 1.979      |  35.1 | 46.39
-Neigh   | 0.61154    | 0.62212    | 0.63307    |   1.0 | 17.51
-Comm    | 0.18944    | 0.24549    | 0.29196    |   7.9 |  6.91
-Output  | 0.0050066  | 0.011804   | 0.032134   |  10.8 |  0.33
-Modify  | 0.52282    | 0.60522    | 0.69588    |   7.9 | 17.03
-Other   |            | 0.02359    |            |       |  0.66
-
-Nlocal:    11 ave 44 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Nghost:    33 ave 44 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs:    205.75 ave 823 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 823
-Ave neighs/atom = 18.7045
-Ave special neighs/atom = 9.77273
-Neighbor list builds = 10000
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1

@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000181113 secs
+  read_data CPU = 0.0251833 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
+87.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031135   | 0.031135   | 0.031135   |   0.0 |  9.13
+Bond    | 0.12623    | 0.12623    | 0.12623    |   0.0 | 37.01
+Kspace  | 0.036491   | 0.036491   | 0.036491   |   0.0 | 10.70
+Neigh   | 0.046395   | 0.046395   | 0.046395   |   0.0 | 13.60
+Comm    | 0.0025396  | 0.0025396  | 0.0025396  |   0.0 |  0.74
+Output  | 0.07775    | 0.07775    | 0.07775    |   0.0 | 22.80
+Modify  | 0.019219   | 0.019219   | 0.019219   |   0.0 |  5.64
+Other   |            | 0.001306   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    740 ave 740 max 740 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4

@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000178751 secs
+  read_data CPU = 0.0385782 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00023773 | 0.0077322  | 0.016042   |   8.4 |  2.85
+Bond    | 0.00073385 | 0.032108   | 0.08446    |  19.4 | 11.84
+Kspace  | 0.041659   | 0.098095   | 0.13373    |  12.3 | 36.16
+Neigh   | 0.028894   | 0.029247   | 0.029558   |   0.1 | 10.78
+Comm    | 0.012367   | 0.013642   | 0.01503    |   0.9 |  5.03
+Output  | 0.032475   | 0.040504   | 0.061019   |   5.9 | 14.93
+Modify  | 0.032934   | 0.049086   | 0.0577     |   4.3 | 18.10
+Other   |            | 0.0008281  |            |       |  0.31
+
+Nlocal:    11 ave 21 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    32.5 ave 43 max 23 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    185 ave 376 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1

@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000217102 secs
+  read_data CPU = 0.00630778 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
+91.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031941   | 0.031941   | 0.031941   |   0.0 |  9.17
+Bond    | 0.13031    | 0.13031    | 0.13031    |   0.0 | 37.42
+Kspace  | 0.037554   | 0.037554   | 0.037554   |   0.0 | 10.78
+Neigh   | 0.047397   | 0.047397   | 0.047397   |   0.0 | 13.61
+Comm    | 0.0025814  | 0.0025814  | 0.0025814  |   0.0 |  0.74
+Output  | 0.083526   | 0.083526   | 0.083526   |   0.0 | 23.98
+Modify  | 0.013602   | 0.013602   | 0.013602   |   0.0 |  3.91
+Other   |            | 0.001336   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    818 ave 818 max 818 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4

@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000163256 secs
+  read_data CPU = 0.0244579 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00014252 | 0.0090715  | 0.021332   |   9.6 |  3.56
+Bond    | 0.00047028 | 0.037261   | 0.10789    |  22.7 | 14.62
+Kspace  | 0.051006   | 0.12756    | 0.1693     |  13.6 | 50.04
+Neigh   | 0.035644   | 0.036088   | 0.036523   |   0.2 | 14.16
+Comm    | 0.013984   | 0.016074   | 0.018676   |   1.6 |  6.31
+Output  | 0.0002816  | 0.00033726 | 0.00044251 |   0.0 |  0.13
+Modify  | 0.023697   | 0.027803   | 0.033552   |   2.5 | 10.91
+Other   |            | 0.0007123  |            |       |  0.28
+
+Nlocal:    11 ave 29 max 0 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Nghost:    25 ave 31 max 12 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:    204.5 ave 443 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/momentum/in.momentum

@@ -0,0 +1,65 @@
+# Test compute momentum with by comparing it's output with compute reduce
+
+# Script will output the two computations of the total momentum as
+# thermo vars - they should be identical
+
+# 3D LJ Poiseuille flow simulation
+dimension	3
+boundary	p p p
+
+atom_style	atomic
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+# create geometry
+lattice		hcp 0.5
+region		box block 0 20 0 10 0 10
+create_box	3 box
+create_atoms	1 box
+
+mass		1 1.0
+mass		2 1.0
+mass		3 1.0
+
+# LJ potentials
+pair_style	lj/cut 1.0
+pair_coeff	* * 1.0 1.0 1.0
+
+# define groups
+region	     1 block INF INF INF 1.0 INF INF
+group	     lower region 1
+region	     2 block INF INF 9.0 INF INF INF
+group	     upper region 2
+group	     boundary union lower upper
+group	     liquid subtract all boundary
+
+set	     group lower type 2
+set	     group upper type 3
+
+# temperature settings
+compute      mobile liquid temp
+velocity     liquid create 1.0 100 temp mobile
+fix          1 all nve
+fix          2 liquid temp/rescale 200 1.0 2.0 0.02 1.0
+fix_modify   2 temp mobile
+
+velocity     boundary set 0.0 0.0 0.0
+fix	     4 lower setforce 0.0 0.0 0.0
+fix	     5 upper setforce 0.0 0.0 0.0
+fix	     6 liquid addforce 0.1 0.0 0.0
+
+# Compute total momentum
+compute mom liquid momentum
+
+# Comparison (momentum variables + compute reduce)
+variable mx atom mass*vx
+variable my atom mass*vy
+variable mz atom mass*vz
+compute mom_red liquid reduce sum v_mx v_my v_mz
+
+# Run
+timestep	0.003
+thermo		1000
+thermo_style custom step c_mom_red[*] c_mom[*]
+
+run		100000

examples/kim/.gitignore

@@ -0,0 +1 @@
+/kim.log

examples/kim/in.kim-ex.melt

@@ -14,20 +14,14 @@ variable	xx equal 20*$x
 variable	yy equal 20*$y
 variable	zz equal 20*$z
 
-units		metal
+kim_init	LennardJones_Ar real
-atom_style	atomic
-newton          on
 
 lattice		fcc 4.4300
 region		box block 0 ${xx} 0 ${yy} 0 ${zz}
 create_box	1 box
 create_atoms	1 box
 
-#pair_style	lj/cut 8.1500
+kim_interactions Ar
-#pair_coeff	1 1 0.0104 3.4000
-
-pair_style      kim LennardJones_Ar
-pair_coeff      * * Ar
 
 mass		1 39.95
 velocity	all create 200.0 232345 loop geom

examples/kim/in.kim-pm-query.melt

@@ -0,0 +1,46 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+kim_query       a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
+
+lattice		fcc ${a0}
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions Si
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100

examples/kim/in.kim-pm.melt

@@ -0,0 +1,45 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+
+lattice		fcc 4.4300
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions Si
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100

examples/kim/in.kim-sm.melt

@@ -0,0 +1,45 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Simulator Model (PM)
+# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# See https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+
+lattice		fcc 4.4300
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions O
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100

examples/kim/in.kim.lj.lmp.newton-off

@@ -1,35 +0,0 @@
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-newton          off
-
-lattice		fcc 4.4300
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-pair_style	lj/cut 8.1500
-pair_coeff	1 1 0.0104 3.4000
-
-#pair_style      kim LennardJones_Ar
-#pair_coeff      * * Ar
-
-mass		1 39.95
-velocity	all create 200.0 232345 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
-
-run 		100

examples/kim/in.kim.lj.newton-off

@@ -1,41 +0,0 @@
-# 3d Lennard-Jones melt
-#
-# This example requires that the example models provided with
-# the kim-api package are installed.  see the ./lib/kim/README or
-# ./lib/kim/Install.py files for details on how to install these
-# example models.
-#
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-newton          off
-
-lattice		fcc 4.4300
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-#pair_style	lj/cut 8.1500
-#pair_coeff	1 1 0.0104 3.4000
-
-pair_style      kim LennardJones_Ar
-pair_coeff      * * Ar
-
-mass		1 39.95
-velocity	all create 200.0 232345 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
-
-run 		100

examples/kim/in.lammps.melt

@@ -8,9 +8,7 @@ variable	xx equal 20*$x
 variable	yy equal 20*$y
 variable	zz equal 20*$z
 
-units		metal
+units		real
-atom_style	atomic
-newton          on
 
 lattice		fcc 4.4300
 region		box block 0 ${xx} 0 ${yy} 0 ${zz}

examples/kim/in.query

@@ -1,11 +0,0 @@
-
-# example for performing a query to the OpenKIM test database to retrieve
-# a parameter to be used in the input. here it requests the aluminium
-# lattice constant for a specific test used for a specific model and then
-# assigns it to the variable 'latconst'
-
-units metal
-info variables out log
-kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
-info variables out log
-lattice fcc ${latconst}

examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1

@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.004499 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
-99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5638     | 2.5638     | 2.5638     |   0.0 | 87.54
-Neigh   | 0.31935    | 0.31935    | 0.31935    |   0.0 | 10.90
-Comm    | 0.006833   | 0.006833   | 0.006833   |   0.0 |  0.23
-Output  | 0.000107   | 0.000107   | 0.000107   |   0.0 |  0.00
-Modify  | 0.027806   | 0.027806   | 0.027806   |   0.0 |  0.95
-Other   |            | 0.01091    |            |       |  0.37
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2370499
-Ave neighs/atom = 74.0781
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03

examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4

@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.001039 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s
-99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.65171    | 0.65891    | 0.67656    |   1.3 | 84.63
-Neigh   | 0.07924    | 0.079548   | 0.07997    |   0.1 | 10.22
-Comm    | 0.006755   | 0.0069015  | 0.007072   |   0.2 |  0.89
-Output  | 4.6e-05    | 9.725e-05  | 0.000203   |   0.0 |  0.01
-Modify  | 0.006841   | 0.006941   | 0.007015   |   0.1 |  0.89
-Other   |            | 0.02618    |            |       |  3.36
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    630904 ave 632094 max 628209 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 2523614
-Ave neighs/atom = 78.8629
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1

@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003479 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9892     | 1.9892     | 1.9892     |   0.0 | 91.26
-Neigh   | 0.14506    | 0.14506    | 0.14506    |   0.0 |  6.65
-Comm    | 0.011049   | 0.011049   | 0.011049   |   0.0 |  0.51
-Output  | 9.1e-05    | 9.1e-05    | 9.1e-05    |   0.0 |  0.00
-Modify  | 0.02347    | 0.02347    | 0.02347    |   0.0 |  1.08
-Other   |            | 0.01094    |            |       |  0.50
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2126875
-Ave neighs/atom = 66.4648
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:02

examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4

@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000919 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s
-99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.55365    | 0.5566     | 0.55868    |   0.2 | 87.63
-Neigh   | 0.041495   | 0.0418     | 0.04211    |   0.1 |  6.58
-Comm    | 0.019086   | 0.021075   | 0.023898   |   1.2 |  3.32
-Output  | 4.4e-05    | 5.025e-05  | 6e-05      |   0.0 |  0.01
-Modify  | 0.009315   | 0.0093595  | 0.009422   |   0.0 |  1.47
-Other   |            | 0.006263   |            |       |  0.99
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    531719 ave 533273 max 529395 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 2126875
-Ave neighs/atom = 66.4648
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/kim/log.06Feb2019.in.kim.lj.newton-off.1

@@ -1,59 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003446 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.6562     | 2.6562     | 2.6562     |   0.0 | 88.05
-Neigh   | 0.31903    | 0.31903    | 0.31903    |   0.0 | 10.58
-Comm    | 0.00634    | 0.00634    | 0.00634    |   0.0 |  0.21
-Output  | 9.1e-05    | 9.1e-05    | 9.1e-05    |   0.0 |  0.00
-Modify  | 0.024723   | 0.024723   | 0.024723   |   0.0 |  0.82
-Other   |            | 0.01032    |            |       |  0.34
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03

examples/kim/log.06Feb2019.in.kim.lj.newton-off.4

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000921 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.77867    | 0.77906    | 0.7794     |   0.0 | 87.52
-Neigh   | 0.087831   | 0.088176   | 0.088805   |   0.1 |  9.91
-Comm    | 0.006358   | 0.0065898  | 0.006815   |   0.3 |  0.74
-Output  | 4.9e-05    | 5.975e-05  | 6.8e-05    |   0.0 |  0.01
-Modify  | 0.010265   | 0.010429   | 0.010678   |   0.2 |  1.17
-Other   |            | 0.005874   |            |       |  0.66
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/kim/log.06Feb2019.in.kim.lj.newton-on.1

@@ -1,59 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003089 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.6786     | 2.6786     | 2.6786     |   0.0 | 87.58
-Neigh   | 0.33105    | 0.33105    | 0.33105    |   0.0 | 10.82
-Comm    | 0.012602   | 0.012602   | 0.012602   |   0.0 |  0.41
-Output  | 9.5e-05    | 9.5e-05    | 9.5e-05    |   0.0 |  0.00
-Modify  | 0.024858   | 0.024858   | 0.024858   |   0.0 |  0.81
-Other   |            | 0.01132    |            |       |  0.37
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03

examples/kim/log.06Feb2019.in.kim.lj.newton-on.4

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000893 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
-99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.76173    | 0.76349    | 0.76597    |   0.2 | 84.53
-Neigh   | 0.088773   | 0.088938   | 0.089074   |   0.0 |  9.85
-Comm    | 0.032018   | 0.03452    | 0.03638    |   0.9 |  3.82
-Output  | 4e-05      | 4.425e-05  | 5.2e-05    |   0.0 |  0.00
-Modify  | 0.009278   | 0.0093917  | 0.009528   |   0.1 |  1.04
-Other   |            | 0.006797   |            |       |  0.75
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/kim/log.22Mar2019.query.g++.1

@@ -1,34 +0,0 @@
-LAMMPS (28 Feb 2019)
-
-# example for performing a query to the OpenKIM test database to retrieve
-# a parameter to be used in the input. here it requests the aluminium
-# lattice constant for a specific test used for a specific model and then
-# assigns it to the variable 'latconst'
-
-units metal
-info variables out log
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-Printed on Fri Mar 22 20:00:56 2019
-
-
-Variable information:
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-
-kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
-info variables out log
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-Printed on Fri Mar 22 20:00:57 2019
-
-
-Variable information:
-Variable[  0]: latconst  ,  style = string    ,  def = 4.03208274841
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-
-lattice fcc ${latconst}
-lattice fcc 4.03208274841
-Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
-Total wall time: 0:00:00

lib/kim/Install.py

@@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
 # settings
 
 thisdir = fullpath('.')
-version = "kim-api-2.0.2"
+version = "kim-api-2.1.1"
 
 # help message
 
@@ -39,11 +39,8 @@ make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditt
 make lib-kim args="-b -a everything"   # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005"    # only add one model or model driver
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
 See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+https://openkim.org/browse/models
 """
 
 pgroup = parser.add_mutually_exclusive_group()
@@ -132,7 +129,7 @@ if buildflag:
 
   # build kim-api
   print("Building kim-api ...")
-  cmd = 'cd "%s/%s/build" && make' % (thisdir, version)
+  cmd = 'cd "%s/%s/build" && make -j2' % (thisdir, version)
   txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   if verboseflag:
     print(txt.decode("UTF-8"))
@@ -140,7 +137,7 @@ if buildflag:
   # install kim-api
 
   print("Installing kim-api ...")
-  cmd = 'cd "%s/%s/build" && make install' % (thisdir, version)
+  cmd = 'cd "%s/%s/build" && make -j2 install' % (thisdir, version)
   txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   if verboseflag:
     print(txt.decode("UTF-8"))

lib/kim/README

@@ -1,11 +1,11 @@
-This directory contains build settings for the KIM API library which
+This directory contains build settings for the KIM API library which is
-is required to use the KIM package and its pair_style kim command in a
+required to use the KIM package and its kim_init, kim_interactions, kim_query,
-LAMMPS input script.
+and pair_kim commands in a LAMMPS input script.
 
 Information about the KIM project can be found at https://openkim.org.
 The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn).
 Ryan Elliott is the main developer for the KIM API and he also
-maintains the code that implements the pair_style kim command.
+maintains the code that implements the KIM commands.
 
 You can type "make lib-kim" from the src directory to see help on
 how to download and build this library via make commands, or you can
@@ -13,11 +13,9 @@ do the same thing by typing "python Install.py" from within this
 directory, or you can do it manually by following the instructions
 below.
 
-As of KIM API version 2, the KIM package also provides a LAMMPS command
+Use of the kim_query command requires that the CURL library (libcurl)
-to perform queries through the OpenKIM web API. This feature requires
+development package and its configuration query tool, curl-config, are
-that the CURL library (libcurl) development package and its configuration
+installed. The provided Makefile.lammps is set up to automatically detect this.
-query tool, curl-config, are installed. The provided Makefile.lammps
-is set up to automatically detect this.
 
 -----------------
 
@@ -40,8 +38,8 @@ $ cmake ..  -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-X.Y.Z
 
 3. Build and install the kim-api and model
 
-$ make
+$ make -j2
-$ make install
+$ make -j2 install
 
 4. Remove source and build files
 
@@ -53,7 +51,7 @@ $ rm -rf kim-api-X.Y.Z.txz
    desired value)
 
 $ source ${PWD}/kim-api-X.Y.Z/bin/kim-api-activate
-$ kim-api-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
+$ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002
 
 
 -----------------

lib/poems/system.h

@@ -15,7 +15,6 @@
  *      CONTACT:        anderk5@rpi.edu                                    *
  *_________________________________________________________________________*/
 
- 
 #ifndef SYSTEM_H
 #define SYSTEM_H
 
@@ -31,7 +30,6 @@
 #include "workspace.h"
 #include "matrixfun.h"
 #include "onsolver.h"
-#include "system.h"
 #include "inertialframe.h"
 #include "rigidbody.h"
 #include "revolutejoint.h"

src/ASPHERE/compute_erotate_asphere.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "compute_erotate_asphere.h"
+#include <mpi.h>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -20,7 +20,6 @@
 #include "atom_vec_tri.h"
 #include "update.h"
 #include "force.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/ASPHERE/compute_temp_asphere.cpp

@@ -15,9 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_asphere.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -26,7 +26,6 @@
 #include "domain.h"
 #include "modify.h"
 #include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/ASPHERE/fix_nh_asphere.cpp

@@ -15,15 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "math_extra.h"
 #include "fix_nh_asphere.h"
+#include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/ASPHERE/fix_nph_asphere.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_asphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 

src/ASPHERE/fix_npt_asphere.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_asphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 

src/ASPHERE/fix_nve_asphere.cpp

@@ -15,16 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "force.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/ASPHERE/fix_nve_asphere_noforce.cpp

@@ -11,16 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "fix_nve_asphere_noforce.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "group.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/ASPHERE/fix_nve_line.cpp

@@ -11,9 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_line.h"
 #include "atom.h"
 #include "atom_vec_line.h"

src/ASPHERE/fix_nve_tri.cpp

@@ -11,9 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_tri.h"
 #include "math_extra.h"
 #include "atom.h"

src/ASPHERE/fix_nvt_asphere.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_asphere.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"

src/ASPHERE/pair_gayberne.cpp

@@ -15,11 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gayberne.h"
+#include <mpi.h>
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,7 +25,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "integrate.h"
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"

src/ASPHERE/pair_line_lj.cpp

@@ -11,11 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_line_lj.h"
+#include <cmath>
 #include "atom.h"
 #include "atom_vec_line.h"
 #include "force.h"

src/ASPHERE/pair_resquared.cpp

@@ -15,11 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_resquared.h"
+#include <mpi.h>
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,7 +25,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "integrate.h"
 #include "memory.h"
 #include "error.h"
 

src/ASPHERE/pair_tri_lj.cpp

@@ -11,11 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tri_lj.h"
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_tri.h"

src/BODY/body_nparticle.cpp

@@ -11,8 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_nparticle.h"
+#include <cstring>
+#include <cstdlib>
+#include "my_pool_chunk.h"
 #include "math_extra.h"
 #include "atom_vec_body.h"
 #include "atom.h"

src/BODY/body_rounded_polygon.cpp

@@ -15,8 +15,10 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_rounded_polygon.h"
+#include <cmath>
+#include <cstring>
+#include "my_pool_chunk.h"
 #include "atom_vec_body.h"
 #include "atom.h"
 #include "force.h"

src/BODY/body_rounded_polyhedron.cpp

@@ -15,12 +15,14 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_rounded_polyhedron.h"
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include "my_pool_chunk.h"
 #include "atom_vec_body.h"
 #include "atom.h"
 #include "force.h"
-#include "domain.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"

src/BODY/compute_body_local.cpp

@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "compute_body_local.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body.h"
 #include "update.h"
-#include "domain.h"
 #include "force.h"
-#include "bond.h"
 #include "memory.h"
 #include "error.h"
 

src/BODY/compute_temp_body.cpp

@@ -16,9 +16,9 @@
    based on ComputeTempAsphere
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_body.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_body.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
@@ -27,7 +27,6 @@
 #include "domain.h"
 #include "modify.h"
 #include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/BODY/fix_nh_body.cpp

@@ -16,15 +16,10 @@
    based on FixNHAsphere
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "math_extra.h"
 #include "fix_nh_body.h"
+#include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
-#include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/BODY/fix_nph_body.cpp

@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_body.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 

src/BODY/fix_npt_body.cpp

@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_body.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 

src/BODY/fix_nve_body.cpp

@@ -11,16 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_body.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
-#include "force.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/BODY/fix_nvt_body.cpp

@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_body.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"

src/BODY/fix_wall_body_polygon.cpp

@@ -15,19 +15,15 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_body_polygon.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polygon.h"
 #include "domain.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "respa.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"

src/BODY/fix_wall_body_polyhedron.cpp

@@ -15,19 +15,15 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_body_polyhedron.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polyhedron.h"
 #include "domain.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "respa.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"

src/BODY/pair_body_nparticle.cpp

@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_nparticle.h"
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"

src/BODY/pair_body_rounded_polygon.cpp

@@ -18,11 +18,10 @@
          the contact history for friction forces.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_rounded_polygon.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"

src/BODY/pair_body_rounded_polyhedron.cpp

@@ -20,12 +20,10 @@
          the contact history for friction forces.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_rounded_polyhedron.h"
-#include "math_extra.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polyhedron.h"
@@ -41,7 +39,6 @@
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
-using namespace MathExtra;
 using namespace MathConst;
 
 #define DELTA 10000

src/CLASS2/angle_class2.cpp

@@ -15,10 +15,10 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "angle_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "angle_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/CLASS2/angle_class2.h

@@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2)
 #ifndef LMP_ANGLE_CLASS2_H
 #define LMP_ANGLE_CLASS2_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {

src/CLASS2/bond_class2.cpp

@@ -15,12 +15,11 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_class2.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/CLASS2/bond_class2.h

@@ -20,7 +20,6 @@ BondStyle(class2,BondClass2)
 #ifndef LMP_BOND_CLASS2_H
 #define LMP_BOND_CLASS2_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {

src/CLASS2/dihedral_class2.cpp

@@ -15,14 +15,13 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "dihedral_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "math_const.h"

src/CLASS2/dihedral_class2.h

@@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2)
 #ifndef LMP_DIHEDRAL_CLASS2_H
 #define LMP_DIHEDRAL_CLASS2_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {

src/CLASS2/improper_class2.cpp

@@ -15,14 +15,13 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "improper_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "improper_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "math_const.h"