Commit 16400661 authored by Dr. Nandor Tamaskovics's avatar Dr. Nandor Tamaskovics
Browse files

Merge remote-tracking branch 'lammps-origin/master' into lammps-tools-doxygen

parents 86ed5559 e798cdf3

cmake/CMakeLists.txt

+11 −8
Original line number Diff line number Diff line
@@ -198,14 +198,13 @@ if(ENABLE_PYTHON) 
  add_definitions(-DLMP_PYTHON)

  include_directories(${PYTHON_INCLUDE_DIR})

  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})

  if(BUILD_SHARED_LIBS)

    if(NOT PYTHON_INSTDIR)

      execute_process(COMMAND ${PYTHON_EXECUTABLE}

        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"

        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)

    endif()

    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})

  if(NOT BUILD_SHARED_LIBS)

    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")

  endif()

endif()
@@ -401,6 +400,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD 
      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)

    elseif(PKG_LIB STREQUAL colvars)

      target_compile_options(colvars PRIVATE -DLEPTON)

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

      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)

    else()

      target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})

    endif()

doc/src/Section_commands.txt

+16 −15
Original line number Diff line number Diff line
@@ -619,7 +619,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. 
"pour"_fix_pour.html,

"press/berendsen"_fix_press_berendsen.html,

"print"_fix_print.html,

"property/atom"_fix_property_atom.html,

"property/atom (k)"_fix_property_atom.html,

"python/invoke"_fix_python_invoke.html,

"python/move"_fix_python_move.html,

"qeq/comb (o)"_fix_qeq_comb.html,
@@ -669,7 +669,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. 
"wall/harmonic"_fix_wall.html,

"wall/lj1043"_fix_wall.html,

"wall/lj126"_fix_wall.html,

"wall/lj93"_fix_wall.html,

"wall/lj93 (k)"_fix_wall.html,

"wall/piston"_fix_wall_piston.html,

"wall/reflect (k)"_fix_wall_reflect.html,

"wall/region"_fix_wall_region.html,
@@ -684,14 +684,14 @@ package"_Section_start.html#start_3. 
"atc"_fix_atc.html,

"ave/correlate/long"_fix_ave_correlate_long.html,

"colvars"_fix_colvars.html,

"dpd/energy"_fix_dpd_energy.html,

"dpd/energy (k)"_fix_dpd_energy.html,

"drude"_fix_drude.html,

"drude/transform/direct"_fix_drude_transform.html,

"drude/transform/reverse"_fix_drude_transform.html,

"edpd/source"_fix_dpd_source.html,

"eos/cv"_fix_eos_cv.html,

"eos/table"_fix_eos_table.html,

"eos/table/rx"_fix_eos_table_rx.html,

"eos/table/rx (k)"_fix_eos_table_rx.html,

"filter/corotate"_fix_filter_corotate.html,

"flow/gauss"_fix_flow_gauss.html,

"gle"_fix_gle.html,
@@ -729,12 +729,12 @@ package"_Section_start.html#start_3. 
"qeq/reax (ko)"_fix_qeq_reax.html,

"qmmm"_fix_qmmm.html,

"qtb"_fix_qtb.html,

"reax/c/bonds"_fix_reax_bonds.html,

"reax/c/species"_fix_reaxc_species.html,

"reax/c/bonds (k)"_fix_reax_bonds.html,

"reax/c/species (k)"_fix_reaxc_species.html,

"rhok"_fix_rhok.html,

"rx"_fix_rx.html,

"rx (k)"_fix_rx.html,

"saed/vtk"_fix_saed_vtk.html,

"shardlow"_fix_shardlow.html,

"shardlow (k)"_fix_shardlow.html,

"smd"_fix_smd.html,

"smd/adjust/dt"_fix_smd_adjust_dt.html,

"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
@@ -907,7 +907,7 @@ KOKKOS, o = USER-OMP, t = OPT. 
"none"_pair_none.html,

"zero"_pair_zero.html,

"hybrid"_pair_hybrid.html,

"hybrid/overlay"_pair_hybrid.html,

"hybrid/overlay (k)"_pair_hybrid.html,

"adp (o)"_pair_adp.html,

"airebo (oi)"_pair_airebo.html,

"airebo/morse (oi)"_pair_airebo.html,
@@ -1026,7 +1026,7 @@ KOKKOS, o = USER-OMP, t = OPT. 
"vashishta/table (o)"_pair_vashishta.html,

"yukawa (gok)"_pair_yukawa.html,

"yukawa/colloid (go)"_pair_yukawa_colloid.html,

"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)

"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)



These are additional pair styles in USER packages, which can be used

if "LAMMPS is built with the appropriate
@@ -1039,13 +1039,13 @@ package"_Section_start.html#start_3. 
"coul/diel (o)"_pair_coul_diel.html,

"coul/long/soft (o)"_pair_lj_soft.html,

"dpd/fdt"_pair_dpd_fdt.html,

"dpd/fdt/energy"_pair_dpd_fdt.html,

"dpd/fdt/energy (k)"_pair_dpd_fdt.html,

"eam/cd (o)"_pair_eam.html,

"edip (o)"_pair_edip.html,

"edip/multi"_pair_edip.html,

"edpd"_pair_meso.html,

"eff/cut"_pair_eff.html,

"exp6/rx"_pair_exp6_rx.html,

"exp6/rx (k)"_pair_exp6_rx.html,

"extep"_pair_extep.html,

"gauss/cut"_pair_gauss.html,

"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
@@ -1072,7 +1072,7 @@ package"_Section_start.html#start_3. 
"morse/smooth/linear"_pair_morse.html,

"morse/soft"_pair_morse.html,

"multi/lucy"_pair_multi_lucy.html,

"multi/lucy/rx"_pair_multi_lucy_rx.html,

"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,

"oxdna/coaxstk"_pair_oxdna.html,

"oxdna/excv"_pair_oxdna.html,

"oxdna/hbond"_pair_oxdna.html,
@@ -1089,6 +1089,7 @@ package"_Section_start.html#start_3. 
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,

"smd/ulsph"_pair_smd_ulsph.html,

"smtbq"_pair_smtbq.html,

"snap (k)"_pair_sap.html,

"sph/heatconduction"_pair_sph_heatconduction.html,

"sph/idealgas"_pair_sph_idealgas.html,

"sph/lj"_pair_sph_lj.html,
@@ -1096,7 +1097,7 @@ package"_Section_start.html#start_3. 
"sph/taitwater"_pair_sph_taitwater.html,

"sph/taitwater/morris"_pair_sph_taitwater_morris.html,

"srp"_pair_srp.html,

"table/rx"_pair_table_rx.html,

"table/rx (k)"_pair_table_rx.html,

"tdpd"_pair_meso.html,

"tersoff/table (o)"_pair_tersoff.html,

"thole"_pair_thole.html,
@@ -1251,7 +1252,7 @@ USER-OMP, t = OPT. 
"ewald/disp"_kspace_style.html,

"msm (o)"_kspace_style.html,

"msm/cg (o)"_kspace_style.html,

"pppm (go)"_kspace_style.html,

"pppm (gok)"_kspace_style.html,

"pppm/cg (o)"_kspace_style.html,

"pppm/disp (i)"_kspace_style.html,

"pppm/disp/tip4p"_kspace_style.html,

doc/src/accelerate_kokkos.txt

+7 −7
Original line number Diff line number Diff line
@@ -326,9 +326,9 @@ include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile. 


KOKKOS_DEVICES=Cuda,OpenMP :pre



The suffix “/kk” is equivalent to “/kk/device”, and for Kokkos CUDA,

using the “-sf kk” in the command line gives the default CUDA version everywhere.

However, if the “/kk/host” suffix is added to a specific style in the input

The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,

using the "-sf kk" in the command line gives the default CUDA version everywhere.

However, if the "/kk/host" suffix is added to a specific style in the input

script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.

Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
@@ -338,16 +338,16 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then: 


mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre



Conversely, if the “-sf kk/host” is used in the command line and then the

“/kk” or “/kk/device” suffix is added to a specific style in your input script,

Conversely, if the "-sf kk/host" is used in the command line and then the

"/kk" or "/kk/device" suffix is added to a specific style in your input script,

then only that specific style will run on the GPU while everything else will

run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU

styles will NOT overlap, except for a special case:



A kspace style and/or molecular topology (bonds, angles, etc.) running on

the host CPU can overlap with a pair style running on the GPU. First compile

with “--default-stream per-thread” added to CCFLAGS in the Kokkos CUDA Makefile.

Then explicitly use the “/kk/host” suffix for kspace and bonds, angles, etc.

with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.

Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.

in the input file and the "kk" suffix (equal to "kk/device") on the command line.

Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"

so CPU/GPU overlap can occur.

doc/src/body.txt

+1 −1
Original line number Diff line number Diff line
@@ -261,7 +261,7 @@ For images created by the "dump image"_dump_image.html command, if the 
polygon consisting of N line segments.  Note that the line segments

are drawn between the N vertices, which does not correspond exactly to

the physical extent of the body (because the "pair_style

rounded/polygon"_pair_body_rounded_polygon.cpp defines finite-size

rounded/polygon"_pair_body_rounded_polygon.html defines finite-size

spheres at those point and the line segments between the spheres are

tangent to the spheres).  The drawn diameter of each line segment is

determined by the {bflag1} parameter for the {body} keyword.  The

doc/src/fix_smd_integrate_tlsph.txt

+2 −5
Original line number Diff line number Diff line
@@ -14,15 +14,12 @@ fix ID group-ID smd/integrate_tlsph keyword values :pre 


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

smd/integrate_tlsph = style name of this fix command

zero or more keyword/value pairs may be appended :ul



keyword = {limit_velocity}  :l

zero or more keyword/value pairs may be appended

keyword = {limit_velocity}  :ul



  {limit_velocity} value = max_vel

    max_vel = maximum allowed velocity :pre



:ule



[Examples:]



fix 1 all smd/integrate_tlsph

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