Loading cmake/CMakeLists.txt +1 −0 Original line number Diff line number Diff line Loading @@ -589,6 +589,7 @@ if(BUILD_TOOLS) enable_language(Fortran) add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f) target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR}) endif() enable_language(C) Loading doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "6 August 2019" "2019-08-06" .TH LAMMPS "7 August 2019" "2019-08-07" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="6 Aug 2019 version"> <META NAME="docnumber" CONTENT="7 Aug 2019 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 6 Aug 2019 version :c,h2 7 Aug 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html Loading doc/src/replicate.txt +9 −6 Original line number Diff line number Diff line Loading @@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre nx,ny,nz = replication factors in each dimension :ulb optional {keyword} = {bbox} :l {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre :ule [Examples:] Loading Loading @@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with image flags that differ by 1. This will allow the bond to be unwrapped appropriately. The optional keyword {bbox} uses a bounding box to only check atoms in replicas that overlap with a processor's sub-domain when assigning atoms to processors, and thus can result in substantial speedups for calculations using a large number of processors. It does require temporarily using more memory. The optional keyword {bbox} uses a bounding box to only check atoms in replicas that overlap with a processor's sub-domain when assigning atoms to processors. It typically results in a substantial speedup when using the replicate command on a large number of processors. It does require temporary use of more memory, specifically that each processor can store all atoms in the entire system before it is replicated. [Restrictions:] Loading examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 0 → 100644 +107 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 kim_init LennardJones_Ar real #=== BEGIN kim-init ========================================== units real #=== END kim-init ============================================ lattice fcc 4.4300 Lattice spacing in x,y,z = 4.43 4.43 4.43 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.004321 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar #=== END kim_interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.45 ghost atom cutoff = 8.45 binsize = 4.225, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.45 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s 98.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59 Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47 Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99 Other | | 0.01547 | | | 0.44 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19911 ave 19911 max 19911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:03 Loading
cmake/CMakeLists.txt +1 −0 Original line number Diff line number Diff line Loading @@ -589,6 +589,7 @@ if(BUILD_TOOLS) enable_language(Fortran) add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f) target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR}) endif() enable_language(C) Loading
doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "6 August 2019" "2019-08-06" .TH LAMMPS "7 August 2019" "2019-08-07" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="6 Aug 2019 version"> <META NAME="docnumber" CONTENT="7 Aug 2019 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 6 Aug 2019 version :c,h2 7 Aug 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html Loading
doc/src/replicate.txt +9 −6 Original line number Diff line number Diff line Loading @@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre nx,ny,nz = replication factors in each dimension :ulb optional {keyword} = {bbox} :l {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre :ule [Examples:] Loading Loading @@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with image flags that differ by 1. This will allow the bond to be unwrapped appropriately. The optional keyword {bbox} uses a bounding box to only check atoms in replicas that overlap with a processor's sub-domain when assigning atoms to processors, and thus can result in substantial speedups for calculations using a large number of processors. It does require temporarily using more memory. The optional keyword {bbox} uses a bounding box to only check atoms in replicas that overlap with a processor's sub-domain when assigning atoms to processors. It typically results in a substantial speedup when using the replicate command on a large number of processors. It does require temporary use of more memory, specifically that each processor can store all atoms in the entire system before it is replicated. [Restrictions:] Loading
examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 0 → 100644 +107 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 kim_init LennardJones_Ar real #=== BEGIN kim-init ========================================== units real #=== END kim-init ============================================ lattice fcc 4.4300 Lattice spacing in x,y,z = 4.43 4.43 4.43 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.004321 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar #=== END kim_interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.45 ghost atom cutoff = 8.45 binsize = 4.225, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.45 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s 98.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59 Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47 Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99 Other | | 0.01547 | | | 0.44 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19911 ave 19911 max 19911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:03
