LAMMPS (17 Apr 2024) WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) # three orthogonal periodic CNTs # demo for replicating triply looped system # infinite loops in x, y, z # includes bonded interactions across box corners # includes bonds, angles, dihedrals, impropers (class2) units real boundary p p p atom_style full pair_style lj/class2 10 angle_style class2 bond_style class2 dihedral_style class2 improper_style class2 read_data three_periodic_CNTs.data.gz Reading data file ... orthogonal box = (0 0 0) to (80.96 80.96 80.96) 1 by 2 by 2 MPI processor grid reading atoms ... 3168 atoms reading velocities ... 3168 velocities scanning bonds ... 3 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 12 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom orthogonal box = (0 0 0) to (80.96 80.96 80.96) 1 by 2 by 2 MPI processor grid reading bonds ... 4752 bonds reading angles ... 9504 angles reading dihedrals ... 19008 dihedrals reading impropers ... 3168 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.064 seconds replicate 2 2 2 bond/periodic Replication is creating a 2x2x2 = 8 times larger system... orthogonal box = (0 0 0) to (161.92 161.92 161.92) 1 by 2 by 2 MPI processor grid bounding box image = (0 0 0) to (0 0 0) bounding box extra memory = 1.62 MB average # of replicas added to proc = 4.50 out of 8 (56.25%) 25344 atoms 38016 bonds 76032 angles 152064 dihedrals 25344 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors special bonds CPU = 0.004 seconds replicate CPU = 0.012 seconds fix 1 all nve run 100 Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Inconsistent image flags (../domain.cpp:1051) Per MPI rank memory allocation (min/avg/max) = 28.69 | 28.69 | 28.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14266.189 1466925.5 1452659.3 -29908.753 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 Loop time of 1.3667 on 4 procs for 100 steps with 25344 atoms Performance: 6.322 ns/day, 3.796 hours/ns, 73.169 timesteps/s, 1.854 Matom-step/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43424 | 0.43539 | 0.43741 | 0.2 | 31.86 Bond | 0.88613 | 0.89013 | 0.90094 | 0.7 | 65.13 Neigh | 0.013198 | 0.013199 | 0.013201 | 0.0 | 0.97 Comm | 0.010742 | 0.020522 | 0.02546 | 4.1 | 1.50 Output | 3.2788e-05 | 3.6302e-05 | 4.4556e-05 | 0.0 | 0.00 Modify | 0.0042029 | 0.0042366 | 0.004267 | 0.0 | 0.31 Other | | 0.003188 | | | 0.23 Nlocal: 6336 ave 6336 max 6336 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 10558 ave 10558 max 10558 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 723394 ave 723394 max 723394 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2893576 Ave neighs/atom = 114.17203 Ave special neighs/atom = 18 Neighbor list builds = 1 Dangerous builds = 0 # write_restart replicate.restart # write_data replicate.data Total wall time: 0:00:01