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
