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) # test of replicating system with periodic bonds in both x and y dimension 2 atom_style molecular read_data data.bond.x.y Reading data file ... orthogonal box = (0 0 -0.5) to (3 3 0.5) 2 by 2 by 1 MPI processor grid reading atoms ... 9 atoms scanning bonds ... 2 = max bonds/atom orthogonal box = (0 0 -0.5) to (3 3 0.5) 2 by 2 by 1 MPI processor grid reading bonds ... 18 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 48 = max # of 1-4 neighbors 8 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.003 seconds #replicate 3 3 1 replicate 3 3 1 bond/periodic Replication is creating a 3x3x1 = 9 times larger system... orthogonal box = (0 0 -0.5) to (9 9 0.5) 2 by 2 by 1 MPI processor grid bounding box image = (0 0 0) to (0 0 0) bounding box extra memory = 0.00 MB average # of replicas added to proc = 6.25 out of 9 (69.44%) 81 atoms 162 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 48 = max # of 1-4 neighbors 24 = max # of special neighbors special bonds CPU = 0.000 seconds replicate CPU = 0.001 seconds mass 1 1.0 velocity all create 0.02 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 4 = max # of 1-2 neighbors 24 = max # of special neighbors special bonds CPU = 0.000 seconds fix 1 all nve write_data tmp.data.x.y 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 7 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.y.*.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.y.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 WARNING: Inconsistent image flags (../domain.cpp:1051) Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.552 | 7.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.02 -1.1250229 0 -1.1052698 -2.9713842 5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897 Loop time of 0.273847 on 4 procs for 5000 steps with 81 atoms Performance: 7887622.810 tau/day, 18258.386 timesteps/s, 1.479 Matom-step/s 92.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0039465 | 0.0042593 | 0.0046129 | 0.4 | 1.56 Bond | 0.0011489 | 0.001207 | 0.0012757 | 0.2 | 0.44 Neigh | 0.00079819 | 0.0008044 | 0.00081324 | 0.0 | 0.29 Comm | 0.024107 | 0.024703 | 0.025269 | 0.3 | 9.02 Output | 0.14406 | 0.18123 | 0.23779 | 8.7 | 66.18 Modify | 0.00089401 | 0.00095321 | 0.0010422 | 0.0 | 0.35 Other | | 0.06069 | | | 22.16 Nlocal: 20.25 ave 22 max 19 min Histogram: 2 0 0 0 0 0 1 0 0 1 Nghost: 81.5 ave 82 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 3 Neighs: 178.5 ave 195 max 165 min Histogram: 2 0 0 0 0 0 0 1 0 1 Total # of neighbors = 714 Ave neighs/atom = 8.8148148 Ave special neighs/atom = 4 Neighbor list builds = 72 Dangerous builds = 0 Total wall time: 0:00:00