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 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)
  4 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)
  4 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)
  4 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 = 0.002 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) = 6.059 | 6.059 | 6.059 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.001         -1.1250229      0             -1.1240599      13.009826    
      5000   0.74931971    -2.233724       0.40158766    -1.1105692      5.6354701    
Loop time of 0.197835 on 4 procs for 5000 steps with 27 atoms

Performance: 10918214.594 tau/day, 25273.645 timesteps/s, 682.388 katom-step/s
88.8% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0018771  | 0.0021131  | 0.0027188  |   0.8 |  1.07
Bond    | 0.00032659 | 0.00038248 | 0.00049555 |   0.0 |  0.19
Neigh   | 0.001385   | 0.0014211  | 0.0014704  |   0.1 |  0.72
Comm    | 0.017163   | 0.017405   | 0.017805   |   0.2 |  8.80
Output  | 0.070971   | 0.11052    | 0.17112    |  12.1 | 55.87
Modify  | 0.00058993 | 0.00067708 | 0.00075608 |   0.0 |  0.34
Other   |            | 0.06532    |            |       | 33.02

Nlocal:           6.75 ave           7 max           6 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost:          59.75 ave          60 max          59 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs:             72 ave          79 max          63 min
Histogram: 1 0 0 0 0 0 2 0 0 1

Total # of neighbors = 288
Ave neighs/atom = 10.666667
Ave special neighs/atom = 1.3333333
Neighbor list builds = 323
Dangerous builds = 0
Total wall time: 0:00:00
