Merge branch 'master' into master

src/GPU/*             @ndtrung81

src/KOKKOS/*          @stanmoore1

src/KIM/*             @ellio167

src/LATTE/*           @cnegre

src/MESSAGE/*         @sjplimp

src/SPIN/*            @julient31

src/USER-CGDNA/*      @ohenrich

src/USER-CGSDK/*      @akohlmey

src/USER-COLVARS/*    @giacomofiorin

src/USER-OMP/*        @akohlmey

src/USER-QMMM/*       @akohlmey

src/USER-REAXC/*      @hasanmetin

src/USER-SCAFACOS/*   @rhalver

src/USER-TALLY/*      @akohlmey

src/USER-UEF/*        @danicholson

src/USER-VTK/*        @rbberger

# individual files in packages

src/GPU/pair_vashishta_gpu.*        @andeplane

src/KOKKOS/pair_vashishta_kokkos.*  @andeplane

src/MANYBODY/pair_vashishta_table.* @andeplane

src/MANYBODY/pair_atm.*             @sergeylishchuk

src/USER-MISC/fix_bond_react.*      @jrgissing

src/USER-MISC/*_grem.*              @dstelter92

src/USER-MISC/compute_stress_mop*.* @RomainVermorel

# core LAMMPS classes

src/lammps.*              @sjplimp

src/pointers.h            @sjplimp

src/atom.*                @sjplimp

src/atom_vec.*            @sjplimp

src/angle.*               @sjplimp

src/bond.*                @sjplimp

src/comm*.*               @sjplimp

src/compute.*             @sjplimp

src/dihedral.*            @sjplimp

src/domain.*              @sjplimp

src/dump*.*               @sjplimp

src/error.*               @sjplimp

src/finish.*              @sjplimp

src/fix.*                 @sjplimp

src/force.*               @sjplimp

src/group.*               @sjplimp

src/improper.*            @sjplimp

src/kspace.*              @sjplimp

src/lmptyp.h              @sjplimp

src/library.*             @sjplimp

src/main.cpp              @sjplimp

src/memory.*              @sjplimp

src/modify.*              @sjplimp

src/molecule.*            @sjplimp

src/my_page.h             @sjplimp

src/my_pool_chunk.h       @sjplimp

src/npair*.*              @sjplimp

src/ntopo*.*              @sjplimp

src/nstencil*.*           @sjplimp

src/neighbor.*            @sjplimp

src/nbin*.*               @sjplimp

src/neigh_*.*             @sjplimp

src/output.*              @sjplimp

src/pair.*                @sjplimp

src/rcb.*                 @sjplimp

src/random_*.*            @sjplimp

src/region*.*             @sjplimp

src/rcb.*                 @sjplimp

src/read*.*               @sjplimp

src/rerun.*               @sjplimp

src/run.*                 @sjplimp

src/respa.*               @sjplimp

src/set.*                 @sjplimp

src/special.*             @sjplimp

src/suffix.h              @sjplimp

src/thermo.*              @sjplimp

src/universe.*            @sjplimp

src/update.*              @sjplimp

src/variable.*            @sjplimp

src/verlet.*              @sjplimp

src/velocity.*            @sjplimp

src/write_data.*          @sjplimp

src/write_restart.*       @sjplimp

# overrides for specific files

src/dump_movie.*          @akohlmey

src/exceptions.h          @rbberger

src/fix_nh.*              @athomps

src/info.*                @akohlmey @rbberger

src/timer.*               @akohlmey

# tools

tools/msi2lmp/*       @akohlmey

tools/emacs/*         @HaoZeke

# cmake

cmake/*               @junghans @rbberger

*~

*.o

*.so

*.lo

*.cu_o

*.ptx

*_ptx.h

.Trashes

ehthumbs.db

Thumbs.db

.clang-format

#cmake

/build*

README			   this file

LICENSE			   the GNU General Public License (GPL)

bench			   benchmark problems

couple			   code coupling examples using LAMMPS as a library

cmake			   CMake build system

doc			   documentation

examples		   simple test problems

lib			   libraries LAMMPS can be linked with

Point your browser at any of these files to get started:

doc/Manual.html	           the LAMMPS manual

doc/Section_intro.html	   hi-level introduction to LAMMPS

doc/Section_start.html	   how to build and use LAMMPS

doc/Developer.pdf          LAMMPS developer guide

http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual

http://lammps.sandia.gov/doc/Intro.html          hi-level introduction

http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS

http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS

http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide

You can also create these doc pages locally:

% cd doc

% make html                # creates HTML pages in doc/html

% make pdf                 # creates Manual.pdf and Developer.pdf

# - Find liblammps

# Find the native liblammps headers and libraries.

#

# The following variables will set:

#  LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.

#  LAMMPS_LIBRARIES    - List of libraries when using lammps.

#  LAMMPS_API_DEFINES  - lammps library api defines

#  LAMMPS_VERSION      - lammps library version 

#  LAMMPS_FOUND        - True if liblammps found.

#

# In addition a LAMMPS::LAMMPS imported target is getting created.

#

#  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

#  http://lammps.sandia.gov, Sandia National Laboratories

#  Steve Plimpton, sjplimp@sandia.gov

#

#  Copyright (2003) Sandia Corporation.  Under the terms of Contract

#  DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

#  certain rights in this software.  This software is distributed under

#  the GNU General Public License.

#

#  See the README file in the top-level LAMMPS directory.

#

find_package(PkgConfig)

pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)

find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)

set(LAMMPS_VERSION @LAMMPS_VERSION@)

set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)

find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)

set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")

set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")

include(FindPackageHandleStandardArgs)

# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE

# if all listed variables are TRUE

find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)

mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)

if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)

  add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)

  set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")

endif()