Merge branch 'master' into fft

src/fix_nh.*              @athomps

src/info.*                @akohlmey @rbberger

src/timer.*               @akohlmey

src/min*                  @sjplimp @stanmoore1

# tools

tools/msi2lmp/*       @akohlmey

find_path (NETCDF_INCLUDE_DIR netcdf.h

  HINTS "${NETCDF_DIR}/include")

mark_as_advanced (NETCDF_INCLUDE_DIR)

set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})

string(REGEX REPLACE "/include/?$" ""

  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})

find_library (NETCDF_LIBRARY NAMES netcdf

  HINTS "${NETCDF_DIR}/lib")

  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)

mark_as_advanced (NETCDF_LIBRARY)

set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake

# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)

#

# - Find PNetCDF

# Find the native PNetCDF includes and library

#

#  PNETCDF_INCLUDES    - where to find netcdf.h, etc

#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF

#  PNETCDF_FOUND       - True if PNetCDF was found

#

# Normal usage would be:

#  find_package (PNetCDF REQUIRED)

#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})

if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)

  # Already in cache, be silent

  set (PNETCDF_FIND_QUIETLY TRUE)

endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)

find_path (PNETCDF_INCLUDES pnetcdf.h

  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")

string(REGEX REPLACE "/include/?$" ""

  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})

find_library (PNETCDF_LIBRARIES

  NAMES pnetcdf

  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)

if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))

  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")

  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)

  find_library(PNETCDF_LIBRARIES

    NAMES pnetcdf

    HINTS ${LD_LIBRARY_PATH})

  if (PNETCDF_LIBRARIES)

    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)

    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"

      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})

    find_path (PNETCDF_INCLUDES pnetcdf.h

      HINTS ${PNETCDF_H_HINT}

      DOC "Path to pnetcdf.h")

  endif()

endif()

# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if

# all listed variables are TRUE

include (FindPackageHandleStandardArgs)

find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)

mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)

if(PKG_USER-NETCDF)

  find_package(NetCDF REQUIRED)

  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.

  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"

  find_package(NetCDF)

  if(NETCDF_FOUND)

    find_package(PNetCDF)

  else(NETCDF_FOUND)

    find_package(PNetCDF REQUIRED)

  endif(NETCDF_FOUND)

  if(NETCDF_FOUND)

    include_directories(${NETCDF_INCLUDE_DIRS})

    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})

  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)

    add_definitions(-DLMP_HAS_NETCDF)

  endif(NETCDF_FOUND)

  if(PNETCDF_FOUND)

    include_directories(${PNETCDF_INCLUDES})

    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})

    add_definitions(-DLMP_HAS_PNETCDF)

  endif(PNETCDF_FOUND)

  add_definitions(-DNC_64BIT_DATA=0x0020)

endif()

.TH LAMMPS "20 November 2019" "2019-11-20"

.TH LAMMPS "9 January 2020" "2020-01-09"

.SH NAME

.B LAMMPS

\- Molecular Dynamics Simulator.