LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-808-g67067cbc80)
  using 1 OpenMP thread(s) per MPI task
# Rhodopsin model

units           real
neigh_modify    delay 5 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
pair_style      lj/charmm/coul/long 8.0 10.0
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data       data.rhodo
Reading data file ...
  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  32000 atoms
  reading velocities ...
  32000 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  8 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  27723 bonds
  reading angles ...
  40467 angles
  reading dihedrals ...
  56829 dihedrals
  reading impropers ...
  1034 impropers
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
    24 = max # of 1-4 neighbors
    26 = max # of special neighbors
  special bonds CPU = 0.009 seconds
  read_data CPU = 0.236 seconds

fix             1 all shake 0.0001 5 0 m 1.0 a 232
Finding SHAKE clusters ...
    1617 = # of size 2 clusters
    3633 = # of size 3 clusters
     747 = # of size 4 clusters
    4233 = # of frozen angles
  find clusters CPU = 0.006 seconds
fix             2 all npt temp 300.0 300.0 100.0                 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

special_bonds   charmm

thermo          50
thermo_style    multi
timestep        2.0

run             100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.24883488
  grid = 25 32 32
  stencil order = 5
  estimated absolute RMS force accuracy = 0.035547797
  estimated relative force accuracy = 0.00010705113
  using double precision FFTW3
  3d grid and FFT values/proc = 41070 25600
Generated 2278 of 2278 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 10 13 13
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =    -25356.2057 KinEng   =     21444.8313 Temp     =       299.0397 
PotEng   =    -46801.0370 E_bond   =      2537.9940 E_angle  =     10921.3742 
E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
E_coul   =    207025.8934 E_long   =   -270403.7333 Press    =      -149.3300 
Volume   =    307995.0335
------------ Step             50 ----- CPU =     6.946771 (sec) -------------
TotEng   =    -25330.0307 KinEng   =     21501.0009 Temp     =       299.8229 
PotEng   =    -46831.0316 E_bond   =      2471.7035 E_angle  =     10836.5102 
E_dihed  =      5239.6319 E_impro  =       227.1218 E_vdwl   =     -1993.2873 
E_coul   =    206797.6807 E_long   =   -270410.3925 Press    =       237.6572 
Volume   =    308031.6762
------------ Step            100 ----- CPU =     14.20402 (sec) -------------
TotEng   =    -25290.7364 KinEng   =     21591.9089 Temp     =       301.0906 
PotEng   =    -46882.6454 E_bond   =      2567.9807 E_angle  =     10781.9571 
E_dihed  =      5198.7492 E_impro  =       216.7864 E_vdwl   =     -1902.6616 
E_coul   =    206659.5159 E_long   =   -270404.9730 Press    =         6.7352 
Volume   =    308134.2286
Loop time of 14.2041 on 1 procs for 100 steps with 32000 atoms

Performance: 1.217 ns/day, 19.728 hours/ns, 7.040 timesteps/s, 225.288 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.001     | 11.001     | 11.001     |   0.0 | 77.45
Bond    | 0.38231    | 0.38231    | 0.38231    |   0.0 |  2.69
Kspace  | 0.6111     | 0.6111     | 0.6111     |   0.0 |  4.30
Neigh   | 1.891      | 1.891      | 1.891      |   0.0 | 13.31
Comm    | 0.021749   | 0.021749   | 0.021749   |   0.0 |  0.15
Output  | 0.00021602 | 0.00021602 | 0.00021602 |   0.0 |  0.00
Modify  | 0.29015    | 0.29015    | 0.29015    |   0.0 |  2.04
Other   |            | 0.006949   |            |       |  0.05

Nlocal:          32000 ave       32000 max       32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          47958 ave       47958 max       47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.431875
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:14
