LAMMPS (17 Apr 2024) # test of replicating system with periodic bonds in x dimension 2 atom_style molecular read_data data.bond.x.non Reading data file ... orthogonal box = (0 0 -0.5) to (3 1 0.5) 1 by 1 by 1 MPI processor grid reading atoms ... 3 atoms scanning bonds ... 1 = max bonds/atom orthogonal box = (0 0 -0.5) to (3 1 0.5) 1 by 1 by 1 MPI processor grid reading bonds ... 2 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.004 seconds replicate 3 3 1 Replication is creating a 3x3x1 = 9 times larger system... orthogonal box = (0 0 -0.5) to (9 3 0.5) 1 by 1 by 1 MPI processor grid 27 atoms 18 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds replicate CPU = 0.001 seconds #replicate 3 3 1 bond/periodic mass 1 1.0 velocity all create 0.001 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 bond_style harmonic bond_coeff 1 50.0 1.0 special_bonds fene Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 1 1 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds fix 1 all nve write_data tmp.data.x.non System init for write_data ... Generated 0 of 0 mixed pair_coeff terms from 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 = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 7 3 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d bin: standard dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 dump_modify 1 pad 5 #dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 #dump_modify 2 pad 5 run 5000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 6.052 | 6.052 | 6.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.001 -1.1250229 0 -1.1240599 13.009826 5000 0.62003692 -2.0147214 0.30861545 -1.1090334 8.0279226 Loop time of 0.0734456 on 1 procs for 5000 steps with 27 atoms Performance: 29409520.548 tau/day, 68077.594 timesteps/s, 1.838 Matom-step/s 94.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0051444 | 0.0051444 | 0.0051444 | 0.0 | 7.00 Bond | 0.00048789 | 0.00048789 | 0.00048789 | 0.0 | 0.66 Neigh | 0.0019333 | 0.0019333 | 0.0019333 | 0.0 | 2.63 Comm | 0.001332 | 0.001332 | 0.001332 | 0.0 | 1.81 Output | 0.063139 | 0.063139 | 0.063139 | 0.0 | 85.97 Modify | 0.00077014 | 0.00077014 | 0.00077014 | 0.0 | 1.05 Other | | 0.0006387 | | | 0.87 Nlocal: 27 ave 27 max 27 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 101 ave 101 max 101 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288 Ave neighs/atom = 10.666667 Ave special neighs/atom = 1.3333333 Neighbor list builds = 322 Dangerous builds = 0 Total wall time: 0:00:00