merged in current master

src/USER-MOFFF/*      @hheenen

src/USER-MOLFILE/*    @akohlmey

src/USER-NETCDF/*     @pastewka

src/USER-PLUMED/*     @gtribello

src/USER-PHONON/*     @lingtikong

src/USER-PTM/*        @pmla

src/USER-OMP/*        @akohlmey

Thus please also have a look at:

* [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15)

* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html)

* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)

## Table of Contents

We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.

How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html)

How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/Howto_github.html)

 for instructions on how to submit your changes or new files through a GitHub pull request

Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.

### Pull Requests

For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.

For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.

Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.

Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that.

You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.

The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.

If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.

Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.

If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.

Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.

  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION

  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD

  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF

  USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ

  USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)

  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS

  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK

  USER-QUIP USER-QMMM)

set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)

set(OTHER_PACKAGES CORESHELL QEQ)

foreach(PKG ${DEFAULT_PACKAGES})

  enable_language(C)

endif()

include_directories(${LAMMPS_SOURCE_DIR})

# do MPI detection after language activation, if MPI for these language is required

find_package(MPI QUIET)

option(BUILD_MPI "Build MPI version" ${MPI_FOUND})

find_package(OpenMP QUIET)

option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})

if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)

if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)

  find_package(OpenMP REQUIRED)

  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")

  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

  endif()

endif()

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)

  find_package(LAPACK)

  find_package(BLAS)

  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)

  include_directories(${SCAFACOS_INCLUDE_DIRS})

endif()

if(PKG_USER-PLUMED)

  find_package(GSL REQUIRED)

  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")

  set(PLUMED_MODE_VALUES static shared runtime)

  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})

  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)

  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)

  option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)

  if(DOWNLOAD_PLUMED)

    include(ExternalProject)

    ExternalProject_Add(plumed_build

      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz 

      URL_MD5 b1be7c48971627febc11c61b70767fc5

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> 

                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                                  )

    ExternalProject_get_property(plumed_build INSTALL_DIR)

    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})

    list(APPEND LAMMPS_DEPS plumed_build)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o

        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})

    elseif(PLUMED_MODE STREQUAL "SHARED")

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})

    endif()

    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")

  else()

    find_package(PkgConfig REQUIRED)

    pkg_check_modules(PLUMED plumed REQUIRED)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)

    elseif(PLUMED_MODE STREQUAL "SHARED")

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)

    endif()

    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

  endif()

  include_directories(${PLUMED_INCLUDE_DIRS})

endif()

if(PKG_USER-MOLFILE)

  add_library(molfile INTERFACE)

  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)

  endif()

endforeach()

# packages that need defines set

foreach(PKG MPIIO)

  if(PKG_${PKG})

    add_definitions(-DLMP_${PKG})

  endif()

endforeach()

# dedicated check for entire contents of accelerator packages

foreach(PKG ${ACCEL_PACKAGES})

  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})

    if(PKG_LIB STREQUAL awpmd)

      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)

    elseif(PKG_LIB STREQUAL h5md)

      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)

      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})

    elseif(PKG_LIB STREQUAL colvars)

      target_compile_options(colvars PRIVATE -DLEPTON)

      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)

  find_package(HDF5 REQUIRED)

  target_link_libraries(h5md ${HDF5_LIBRARIES})

  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})

  include_directories(${HDF5_INCLUDE_DIRS})

endif()

    include_directories(${USER-OMP_SOURCES_DIR})

endif()

# Fix rigid/meso requires RIGID to be installed

if(PKG_USER-SDPD)

  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)

  get_property(hlist GLOBAL PROPERTY FIX)

  if(NOT PKG_RIGID)

    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)

    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)

  endif()

  set_property(GLOBAL PROPERTY FIX "${hlist}")

  include_directories(${USER-SDPD_SOURCES_DIR})

endif()

if(PKG_KOKKOS)

  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)

GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})

include_directories(${LAMMPS_SOURCE_DIR})

include_directories(${LAMMPS_STYLE_HEADERS_DIR})

######################################

  </dl>

  </td>

</tr>

<tr>

  <td><code>BIN2C</code> (CUDA only)</td>

  <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

  <td>(automatic)</td>

</tr>

</tbody>

</table>

</tr>

<tr>

  <td><code>GZIP_EXECUTABLE</code></td>

  <td></td>

  <td>

  </td>

  <td>Path to gzip executable, will automatically pick up the first one in your $PATH.</td>

  <td>(automatic)</td>

</tr>

</tbody>

</table>

</tr>

<tr>

  <td><code>FFMPEG_EXECUTABLE</code></td>

  <td></td>

  <td>

  </td>

  <td>Path to ffmpeg executable, will automatically pick up the first one in your $PATH.</td>

  <td>(automatic)</td>

</tr>

</tbody>

</table>

# pkg-config file for lammps

# https://people.freedesktop.org/~dbn/pkg-config-guide.html

# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c

# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,

# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH

# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig

# Use this on commandline with:

# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp

# Use this in a Makefile:

# myapp: myapp.cpp

# 	$(CC) `pkg-config --cflags --libs lammps` -o $@ $<

# Use this in autotools:

# configure.ac:

# PKG_CHECK_MODULES([LAMMPS], [lammps])

# Makefile.am:

# myapp_CFLAGS = $(LAMMPS_CFLAGS)

# myapp_LDADD = $(LAMMPS_LIBS)

# Use this in CMake:

# CMakeLists.txt:

# find_package(PkgConfig)

# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)

# target_link_libraries(<lib> PkgConfig::LAMMPS)

prefix=@CMAKE_INSTALL_PREFIX@

libdir=@CMAKE_INSTALL_FULL_LIBDIR@

includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@