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 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)
  2 by 2 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)
  2 by 2 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 = 0.003 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%)
  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) = 6.301 | 6.301 | 6.301 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.02          -0.66256988     2.2804444e-06 -0.64330834    -0.59475371   
      5000   0.43110877    -1.1484507      0.168888      -0.56442093    -0.36839692   
Loop time of 0.286423 on 4 procs for 5000 steps with 27 atoms

Performance: 7541285.935 tau/day, 17456.680 timesteps/s, 471.330 katom-step/s
92.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00054941 | 0.00084836 | 0.0013689  |   0.0 |  0.30
Bond    | 0.00034068 | 0.00045816 | 0.00068461 |   0.0 |  0.16
Neigh   | 0.00092076 | 0.00098494 | 0.0010463  |   0.0 |  0.34
Comm    | 0.018151   | 0.018737   | 0.019531   |   0.4 |  6.54
Output  | 0.13261    | 0.19363    | 0.2596     |  10.7 | 67.60
Modify  | 0.00053153 | 0.00071381 | 0.0010268  |   0.0 |  0.25
Other   |            | 0.07105    |            |       | 24.81

Nlocal:           6.75 ave           9 max           5 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:          26.25 ave          28 max          25 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs:           16.5 ave          23 max          10 min
Histogram: 1 1 0 0 0 0 0 0 1 1

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
