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 4 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) = 3.23 | 3.23 | 3.23 Mbytes Step Temp Pzz PotEng Lz 0 3.1494433 -3.4735106 -6.8707307 34 100 1.7914373 6.4805818 -4.8420353 34 200 1.740256 6.6108149 -4.7672571 34 300 1.7663827 6.5188941 -4.8103672 34 400 1.7440644 6.5156543 -4.7769467 34 500 1.7471724 6.5208992 -4.7843928 34 600 1.7320106 6.6557835 -4.7654637 34 700 1.6839043 6.7689759 -4.7045352 34 800 1.7216746 6.66436 -4.7601673 34 900 1.7342542 6.3242367 -4.7790803 34 1000 1.7338566 6.5803438 -4.7854529 34 1100 1.7328856 6.3846366 -4.7902625 34 1200 1.7546906 6.5048137 -4.8213443 34 1300 1.7163891 6.3903221 -4.7665145 34 1400 1.7011627 6.5782672 -4.7517875 34 1500 1.7105234 6.5811813 -4.7677748 34 1600 1.7334403 6.5032837 -4.8067749 34 1700 1.7252102 6.5443871 -4.8058994 34 1800 1.721958 6.3378188 -4.8150073 34 1900 1.6797892 6.6780506 -4.7538618 34 2000 1.7001774 6.3578192 -4.7894018 34 2100 1.7127784 6.3219105 -4.8161059 34 2200 1.696825 6.536793 -4.7946902 34 2300 1.6704578 6.7186933 -4.7609628 34 2400 1.6772498 6.3432817 -4.7778471 34 2500 1.7073862 6.2153226 -4.8299181 34 2600 1.6951557 6.4397257 -4.8156787 34 2700 1.6845984 6.0123544 -4.8136864 34 2800 1.6550565 6.2489392 -4.7829639 34 2900 1.6892315 6.158499 -4.8423004 34 3000 1.6814436 6.07976 -4.8400696 34 3100 1.6387025 6.330166 -4.7878978 34 3200 1.6747855 6.0767043 -4.8481995 34 3300 1.6508768 6.2749233 -4.8181888 34 3400 1.6426364 6.3934935 -4.8223824 34 3500 1.6576512 6.0638185 -4.8559078 34 3600 1.6444173 6.1376573 -4.8463113 34 3700 1.6480039 5.9943705 -4.8601776 34 3800 1.6467212 6.0556591 -4.8722719 34 3900 1.6271804 6.116738 -4.8547278 34 4000 1.6158134 5.9089534 -4.8477829 34 4100 1.6388157 5.9890465 -4.8920284 34 4200 1.6182368 6.0639887 -4.8724963 34 4300 1.647633 5.6333906 -4.9267536 34 4400 1.5856411 6.2675475 -4.8471239 34 4500 1.5773417 6.1789163 -4.8469057 34 4600 1.6181445 5.7988068 -4.922419 34 4700 1.5876712 5.7398111 -4.8853849 34 4800 1.5708353 6.2204997 -4.8718872 34 4900 1.5514708 5.9782256 -4.8523812 34 5000 1.553347 5.9286523 -4.86582 34 Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms Performance: 213265.164 tau/day, 617.087 timesteps/s 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2964 | 5.6236 | 5.8982 | 9.0 | 69.40 Neigh | 1.0562 | 1.1907 | 1.3257 | 8.7 | 14.70 Comm | 0.43963 | 0.98786 | 1.5968 | 42.5 | 12.19 Output | 0.0023124 | 0.004741 | 0.0090873 | 4.0 | 0.06 Modify | 0.018652 | 0.22213 | 0.39884 | 36.4 | 2.74 Other | | 0.07357 | | | 0.91 Nlocal: 1280 ave 1337 max 1211 min Histogram: 1 0 0 0 0 1 1 0 0 1 Nghost: 3416.25 ave 3549 max 3297 min Histogram: 2 0 0 0 0 0 0 0 1 1 Neighs: 74269.8 ave 77932 max 69612 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 297079 Ave neighs/atom = 58.0232 Neighbor list builds = 474 Dangerous builds = 247 write_data data.halfhalf Total wall time: 0:00:08