LAMMPS (22 Sep 2017) using 1 OpenMP thread(s) per MPI task units lj dimension 3 boundary p p p atom_style atomic # truncated and shifted LJ potential pair_style lj/cut 2.5 pair_modify shift yes # fcc lattice lattice fcc 0.9731 Lattice spacing in x,y,z = 1.6019 1.6019 1.6019 region my_box block 0 8.0 0 8.0 0 20.0 create_box 1 my_box Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379) 1 by 1 by 1 MPI processor grid region particles block 0 8.0 0 8.0 0 20.0 create_atoms 1 region particles Created 5120 atoms pair_coeff 1 1 1.0 1.0 2.5 mass 1 1.0 change_box all z final 0.0 34 remap units box orthogonal box = (0 0 0) to (12.8152 12.8152 34) # select particles in one side of the elongated box region left plane 0 0 10 0 0 1 group left region left 2688 atoms in group left velocity left create 6.0 1 mom yes rot yes # simulation parameters neighbor 0.6 bin timestep 0.004 run_style verlet fix ensemble left nve # Note: only move particle in left-hand side fix langevin left langevin 3.0 0.8 100.0 2017 # outout thermo_style custom step temp pzz pe lz thermo 100 # dump dumpXYZ all xyz 100 traj.xyz # run reduced for demonstration purposes # run 10000 run 5000 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.1 ghost atom cutoff = 3.1 binsize = 1.55, bins = 9 9 22 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes Step Temp Pzz PotEng Lz 0 3.1494433 -3.4735106 -6.8707307 34 100 1.7727555 6.5330255 -4.8035477 34 200 1.7462368 7.0070325 -4.7646426 34 300 1.7564888 6.6190123 -4.7894637 34 400 1.7641186 6.609684 -4.8064772 34 500 1.7383511 6.7304936 -4.7708095 34 600 1.731708 6.8574656 -4.7612918 34 700 1.7332167 6.6530919 -4.7670014 34 800 1.7487537 6.5644963 -4.7907458 34 900 1.7353648 6.7115188 -4.7772149 34 1000 1.728878 6.4175719 -4.7797216 34 1100 1.7471488 6.5346083 -4.813376 34 1200 1.7188149 6.2502104 -4.7822235 34 1300 1.7151194 6.792534 -4.7781701 34 1400 1.7406603 6.6639592 -4.8170174 34 1500 1.7090537 6.4677579 -4.770701 34 1600 1.7014954 6.2853535 -4.7679742 34 1700 1.7064354 6.4352857 -4.7812978 34 1800 1.7169971 6.5808758 -4.799426 34 1900 1.6822712 6.3746758 -4.7522464 34 2000 1.7126546 6.534969 -4.8091595 34 2100 1.7086108 6.4679932 -4.8146664 34 2200 1.6974952 6.3802129 -4.8052505 34 2300 1.6868035 6.4009243 -4.7935769 34 2400 1.7107125 6.2318869 -4.8358765 34 2500 1.660241 6.4891487 -4.7661183 34 2600 1.6801816 6.1988356 -4.8024291 34 2700 1.6940298 6.1328187 -4.8290053 34 2800 1.6755061 6.4150693 -4.8145473 34 2900 1.6749928 6.4248792 -4.8213509 34 3000 1.6310737 6.6491291 -4.7673027 34 3100 1.6559915 6.2726719 -4.8109181 34 3200 1.6574579 5.7132029 -4.8189484 34 3300 1.6816136 5.7697439 -4.8652811 34 3400 1.6489483 6.4463349 -4.8247812 34 3500 1.6557974 5.9763333 -4.8383712 34 3600 1.6215459 6.2806534 -4.7954657 34 3700 1.6484987 6.0671609 -4.8470777 34 3800 1.6473922 5.8688108 -4.8555351 34 3900 1.6435957 5.930425 -4.8562076 34 4000 1.6514434 6.1962122 -4.872998 34 4100 1.6138337 6.4808124 -4.8219373 34 4200 1.6215239 5.9467966 -4.8412146 34 4300 1.6129295 5.9377323 -4.8414596 34 4400 1.6020549 6.1104301 -4.8395939 34 4500 1.6047738 6.0816222 -4.8538151 34 4600 1.6053565 6.183466 -4.8686817 34 4700 1.6088152 5.7416542 -4.894114 34 4800 1.5954309 5.694319 -4.8840198 34 4900 1.5582564 6.1199614 -4.8429998 34 5000 1.5786672 5.8813574 -4.8907344 34 Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms Performance: 60873.483 tau/day, 176.139 timesteps/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.269 | 22.269 | 22.269 | 0.0 | 78.45 Neigh | 4.7222 | 4.7222 | 4.7222 | 0.0 | 16.64 Comm | 0.40821 | 0.40821 | 0.40821 | 0.0 | 1.44 Output | 0.0042329 | 0.0042329 | 0.0042329 | 0.0 | 0.01 Modify | 0.88231 | 0.88231 | 0.88231 | 0.0 | 3.11 Other | | 0.1005 | | | 0.35 Nlocal: 5120 ave 5120 max 5120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7768 ave 7768 max 7768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 297167 ave 297167 max 297167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297167 Ave neighs/atom = 58.0404 Neighbor list builds = 474 Dangerous builds = 246 write_data data.halfhalf Total wall time: 0:00:28