Merge branch 'master' into collected-small-changes

    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})

    add_definitions(-DLMP_KIM_CURL)

  endif()

  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)

  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)

  if(DOWNLOAD_KIM)

    message(STATUS "KIM-API v2 download requested - we will build our own")

    message(STATUS "KIM-API download requested - we will build our own")

    enable_language(C)

    enable_language(Fortran)

    include(ExternalProject)

    ExternalProject_Add(kim_build

      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz

      URL_MD5 289c57f0c3bc2a549662283cac1c4ef1

      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz

      URL_MD5 537d9c0abd30f85b875ebb584f9143fa

      BINARY_DIR build

      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}

      )

    ExternalProject_get_property(kim_build INSTALL_DIR)

    set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)

    set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})

    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)

    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})

    list(APPEND LAMMPS_DEPS kim_build)

  else()

    find_package(KIM-API-V2)

    if(NOT KIM-API-V2_FOUND)

      message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")

    find_package(KIM-API)

    if(NOT KIM-API_FOUND)

      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")

    endif()

  endif()

  list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")

  include_directories(${KIM-API-V2_INCLUDE_DIRS})

  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")

  include_directories(${KIM-API_INCLUDE_DIRS})

endif()

if(PKG_MESSAGE)

#

#

# Copyright (c) 2013--2018, Regents of the University of Minnesota.

# Copyright (c) 2013--2019, Regents of the University of Minnesota.

# All rights reserved.

#

# Contributors:

#    Ryan S. Elliott

#

# - Find KIM-API-V2

# - Find KIM-API

#

# sets standard pkg_check_modules variables plus:

#

# KIM-API-V2-CMAKE_C_COMPILER

# KIM-API-V2-CMAKE_CXX_COMPILER

# KIM-API-V2-CMAKE_Fortran_COMPILER

# KIM-API-CMAKE_C_COMPILER

# KIM-API-CMAKE_CXX_COMPILER

# KIM-API-CMAKE_Fortran_COMPILER

#

find_package(PkgConfig REQUIRED)

include(FindPackageHandleStandardArgs)

pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)

pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)

pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)

pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)

pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)

pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)

pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)

pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)

# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE

# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE

# if all listed variables are TRUE

find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)

find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

If DOWNLOAD_KIM is set, the KIM library will be downloaded and built

inside the CMake build directory.  If the KIM library is already on

your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH

environment variable so that libkim-api-v2 can be found.

environment variable so that libkim-api can be found.

[Traditional make]:

"wall/body/polyhedron"_fix_wall_body_polyhedron.html,

"wall/colloid"_fix_wall.html,

"wall/ees"_fix_wall_ees.html,

"wall/gran (o)"_fix_wall_gran.html,

"wall/gran"_fix_wall_gran.html,

"wall/gran/region"_fix_wall_gran_region.html,

"wall/harmonic"_fix_wall.html,

"wall/lj1043"_fix_wall.html,

:line

fix wall/gran command :h3

fix wall/gran/omp command :h3

[Syntax:]

fix ID group-ID wall/gran fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... :pre

fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l

wall/gran = style name of this fix command :l

fstyle = style of force interactions between particles and wall :l

  possible choices: hooke, hooke/history, hertz/history :pre

Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l

Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l

gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l

gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l

xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l

dampflag = 0 or 1 if tangential damping force is excluded or included :l

  possible choices: hooke, hooke/history, hertz/history, granular :pre

fstyle_params = parameters associated with force interaction style :l

  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 

	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 

	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 

	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 

	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  

	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 

	dampflag = 0 or 1 if tangential damping force is excluded or included :pre

  For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre

wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l

args = list of arguments for a particular style :l

  {xplane} or {yplane} or {zplane} args = lo hi

fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0

fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL

fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 :pre

fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 

fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL

fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0

fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre

[Description:]

The nature of the wall/particle interactions are determined by the

{fstyle} setting.  It can be any of the styles defined by the

"pair_style granular"_pair_gran.html commands.  Currently this is

{hooke}, {hooke/history}, or {hertz/history}.  The equation for the

force between the wall and particles touching it is the same as the

corresponding equation on the "pair_style granular"_pair_gran.html doc

page, in the limit of one of the two particles going to infinite

radius and mass (flat wall).  Specifically, delta = radius - r =

overlap of particle with wall, m_eff = mass of particle, and the

effective radius of contact = RiRj/Ri+Rj is just the radius of the

particle.

"pair_style gran/*"_pair_gran.html or the more general "pair_style

granular"_pair_granular.html" commands.  Currently the options are

{hooke}, {hooke/history}, or {hertz/history} for the former, and

{granular} with all the possible options of the associated

{pair_coeff} command for the latter.  The equation for the force

between the wall and particles touching it is the same as the

corresponding equation on the "pair_style gran/*"_pair_gran.html and

"pair_style_granular"_pair_granular.html doc pages, in the limit of

one of the two particles going to infinite radius and mass (flat

wall).  Specifically, delta = radius - r = overlap of particle with

wall, m_eff = mass of particle, and the effective radius of contact =

RiRj/Ri+Rj is set to the radius of the particle.

The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}

have the same meaning and units as those specified with the

"pair_style granular"_pair_gran.html commands.  This means a NULL can

be used for either {Kt} or {gamma_t} as described on that page.  If a

"pair_style gran/*"_pair_gran.html commands.  This means a NULL can be

used for either {Kt} or {gamma_t} as described on that page.  If a

NULL is used for {Kt}, then a default value is used where {Kt} = 2/7

{Kn}.  If a NULL is used for {gamma_t}, then a default value is used

where {gamma_t} = 1/2 {gamma_n}.

All the model choices for cohesion, tangential friction, rolling

friction and twisting friction supported by the "pair_style

granular"_pair_granular.html through its {pair_coeff} command are also

supported for walls. These are discussed in greater detail on the doc

page for "pair_style granular"_pair_granular.html.

Note that you can choose a different force styles and/or different

values for the 6 wall/particle coefficients than for particle/particle

values for the wall/particle coefficients than for particle/particle

interactions.  E.g. if you wish to model the wall as a different

material.

NOTE: As discussed on the doc page for "pair_style

granular"_pair_gran.html, versions of LAMMPS before 9Jan09 used a

gran/*"_pair_gran.html, versions of LAMMPS before 9Jan09 used a

different equation for Hertzian interactions.  This means Hertizian

wall/particle interactions have also changed.  They now include a

sqrt(radius) term which was not present before.  Also the previous

keywords are appended.  Both keywords cannot be used together.

For the {wiggle} keyword, the wall oscillates sinusoidally, similar to

the oscillations of particles which can be specified by the

"fix move"_fix_move.html command.  This is useful in packing

simulations of granular particles.  The arguments to the {wiggle}

keyword specify a dimension for the motion, as well as it's

{amplitude} and {period}.  Note that if the dimension is in the plane

of the wall, this is effectively a shearing motion.  If the dimension

is perpendicular to the wall, it is more of a shaking motion.  A

{zcylinder} wall can only be wiggled in the z dimension.

the oscillations of particles which can be specified by the "fix

move"_fix_move.html command.  This is useful in packing simulations of

granular particles.  The arguments to the {wiggle} keyword specify a

dimension for the motion, as well as it's {amplitude} and {period}.

Note that if the dimension is in the plane of the wall, this is

effectively a shearing motion.  If the dimension is perpendicular to

the wall, it is more of a shaking motion.  A {zcylinder} wall can only

be wiggled in the z dimension.

Each timestep, the position of a wiggled wall in the appropriate {dim}

is set according to this equation:

{vshear} < 0.  In this case, {vshear} is the tangential velocity of

the wall at whatever {radius} has been defined.

:line

Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

functionally the same as the corresponding style without the suffix.

They have been optimized to run faster, depending on your available

hardware, as discussed on the "Speed packages"_Speed_packages.html doc

page.  The accelerated styles take the same arguments and should

produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,

USER-OMP and OPT packages, respectively.  They are only enabled if

LAMMPS was built with those packages.  See the "Build

package"_Build_package.html doc page for more info.

You can specify the accelerated styles explicitly in your input script

by including their suffix, or you can use the "-suffix command-line

switch"_Run_options.html when you invoke LAMMPS, or you can use the

"suffix"_suffix.html command in your input script.

See the "Speed packages"_Speed_packages.html doc page for more

instructions on how to use the accelerated styles effectively.

[Restart, fix_modify, output, run start/stop, minimize info:]

This fix writes the shear friction state of atoms interacting with the

"fix move"_fix_move.html,

"fix wall/gran/region"_fix_wall_gran_region.html,

"pair_style granular"_pair_gran.html

"pair_style gran/*"_pair_gran.html

"pair_style granular"_pair_granular.html

[Default:] none