LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the KIM Portable Model (PM) # SW_StillingerWeber_1985_Si__MO_405512056662_005 # is installed. This can be done with the command # kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 # If this command does not work, you may need to setup your PATH to find the utility. # If you installed the kim-api using the LAMMPS CMake build, you can do the following # (where the current working directory is assumed to be the LAMMPS build directory) # source ./kim_build-prefix/bin/kim-api-activate # If you installed the kim-api using the LAMMPS Make build, you can do the following # (where the current working directory is assumed to be the LAMMPS src directory) # source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate # (where you should relplace X.Y.Z with the appropriate kim-api version number). # # Or, see https://openkim.org/doc/obtaining-models for alternative options. # 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 SW_StillingerWeber_1985_Si__MO_405512056662_005 real #=== BEGIN kim-init ========================================== units real #=== END kim-init ============================================ kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string 4.146581932902336 #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 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 (82.9316 82.9316 82.9316) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.005415 secs kim_interactions Si #=== BEGIN kim_interactions ================================== pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 pair_coeff * * Si #=== 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 = 4.07118 ghost atom cutoff = 4.07118 binsize = 2.03559, bins = 41 41 41 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 4.07118 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 -126084.25 0 -107007.66 1528.8768 100 94.450495 -116016.03 0 -107007.07 2282.2685 Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s 98.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79 Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13 Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02 Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00 Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05 Other | | 0.01396 | | | 0.02 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9667 ave 9667 max 9667 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: 450192 ave 450192 max 450192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450192 Ave neighs/atom = 14.0685 Neighbor list builds = 3 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:16