LAMMPS (17 Apr 2024) # test of replicating system with periodic bonds in xy diagonal direction dimension 2 atom_style molecular read_data data.bond.xy Reading data file ... orthogonal box = (0 0 -0.5) to (3 3 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 3 0.5) 1 by 1 by 1 MPI processor grid reading bonds ... 3 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 2 = max # of 1-3 neighbors 4 = 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 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) 1 by 1 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 = 9.00 out of 9 (100.00%) 27 atoms 27 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 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = 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 1.5 bond_style harmonic bond_coeff 1 50.0 1.414 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 6 = max # of special neighbors special bonds CPU = 0.000 seconds fix 1 all nve write_data tmp.data.xy 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.xy.*.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.xy.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) = 6.302 | 6.302 | 6.302 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.02 -0.66256987 2.2804444e-06 -0.64330834 -0.59475371 5000 0.43110862 -1.1484506 0.16888799 -0.56442095 -0.3683968 Loop time of 0.124095 on 1 procs for 5000 steps with 27 atoms Performance: 17406010.885 tau/day, 40291.692 timesteps/s, 1.088 Matom-step/s 82.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0013734 | 0.0013734 | 0.0013734 | 0.0 | 1.11 Bond | 0.00064058 | 0.00064058 | 0.00064058 | 0.0 | 0.52 Neigh | 0.00090424 | 0.00090424 | 0.00090424 | 0.0 | 0.73 Comm | 0.00081732 | 0.00081732 | 0.00081732 | 0.0 | 0.66 Output | 0.11905 | 0.11905 | 0.11905 | 0.0 | 95.93 Modify | 0.0007252 | 0.0007252 | 0.0007252 | 0.0 | 0.58 Other | | 0.0005888 | | | 0.47 Nlocal: 27 ave 27 max 27 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 45 ave 45 max 45 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66 ave 66 max 66 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66 Ave neighs/atom = 2.4444444 Ave special neighs/atom = 2 Neighbor list builds = 244 Dangerous builds = 0 Total wall time: 0:00:00