LAMMPS (6 Jul 2017)
  using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake

# variables available on command line

variable        mu index -8.1
variable	disp index 0.5
variable        temp index 338.0
variable        lbox index 10.0
variable        spacing index 5.0

# global model settings

units           real
atom_style      full
boundary        p p p
pair_style      lj/cut/coul/long  14
pair_modify     mix arithmetic tail yes
kspace_style    ewald 0.0001
bond_style      harmonic
angle_style     harmonic

# box, start molecules on simple cubic lattice

lattice 	sc ${spacing}
lattice 	sc 5.0
Lattice spacing in x,y,z = 5 5 5
region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region          box block 0 10.0 0 10.0 0 ${lbox} units box
region          box block 0 10.0 0 10.0 0 10.0 units box
create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
  1 by 2 by 2 MPI processor grid

# we can load multiple molecule templates, but don't have to use them all
molecule        co2mol CO2.txt
Read molecule co2mol:
  3 atoms with 2 types
  2 bonds with 1 types
  1 angles with 1 types
  0 dihedrals with 0 types
  0 impropers with 0 types
molecule        h2omol H2O.txt
Read molecule h2omol:
  3 atoms with 2 types
  2 bonds with 1 types
  1 angles with 1 types
  0 dihedrals with 0 types
  0 impropers with 0 types
create_atoms   	0 box mol h2omol 464563 units box
Created 24 atoms

# rigid SPC/E water model

pair_coeff      1 1 0.15535 3.166
pair_coeff      * 2 0.0000 0.0000

bond_coeff      1     1000       1.0
angle_coeff     1      100       109.47

# masses

mass 1 15.9994
mass 2 1.0

# MD settings

group           h2o type 1 2
24 atoms in group h2o
neighbor        2.0 bin
neigh_modify    every 1 delay 1 check yes
velocity       	all create ${temp} 54654
velocity       	all create 338.0 54654
timestep        1.0

minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 2 2 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          338   -4.9610706 9.2628112e-06    18.211756    730.90791 
     100          338   -15.742442   0.14954269     7.579918   -637.49568 
Loop time of 0.0828406 on 4 procs for 100 steps with 24 atoms

98.7% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
        -4.96106135393     -15.5388622715      -15.592899346
  Force two-norm initial, final = 15.474 18.1478
  Force max component initial, final = 5.80042 7.56514
  Final line search alpha, max atom move = 0.00151131 0.0114333
  Iterations, force evaluations = 100 328

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.012844   | 0.025471   | 0.047008   |   8.1 | 30.75
Bond    | 0.00038934 | 0.00046468 | 0.00054336 |   0.0 |  0.56
Kspace  | 0.0061138  | 0.027556   | 0.04014    |   7.8 | 33.26
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.023276   | 0.023636   | 0.023804   |   0.1 | 28.53
Output  | 3.171e-05  | 3.3557e-05 | 3.8147e-05 |   0.0 |  0.04
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.00568    |            |       |  6.86

Nlocal:    6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost:    1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs:    1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1

Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat

fix             mynvt all nvt temp ${temp} ${temp} 100
fix             mynvt all nvt temp 338.0 ${temp} 100
fix             mynvt all nvt temp 338.0 338.0 100
fix             wshake  all shake 0.0001 50 0 b 1 a 1 mol h2omol
  0 = # of size 2 clusters
  0 = # of size 3 clusters
  0 = # of size 4 clusters
  8 = # of frozen angles
# gcmc



run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    518.26667   -15.742442            0    7.4303753    -613.0781 
    1000    369.81793   -54.202686            0   -37.667331    294.98823 
Loop time of 0.199641 on 4 procs for 1000 steps with 24 atoms

Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.017161   | 0.034988   | 0.05833    |   8.0 | 17.53
Bond    | 0.00017357 | 0.00021374 | 0.00027347 |   0.0 |  0.11
Kspace  | 0.018025   | 0.044624   | 0.065613   |   8.4 | 22.35
Neigh   | 0.0029755  | 0.0033154  | 0.0036366  |   0.6 |  1.66
Comm    | 0.059933   | 0.06537    | 0.070709   |   1.5 | 32.74
Output  | 3.4571e-05 | 3.6657e-05 | 4.22e-05   |   0.0 |  0.02
Modify  | 0.043458   | 0.045628   | 0.04767    |   0.9 | 22.86
Other   |            | 0.005465   |            |       |  2.74

Nlocal:    6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost:    1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:    1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2

Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0

variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake

# output

variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify  thermo_temp dynamic/dof yes
thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo          1000

# run

run             20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
    1000    369.81793    295.32434   -54.202686    16.535355   0.23910963       24            0            0            0            0 
    2000    84.544466   -2810.9047   -344.81664    14.364627   0.86677242       87  0.052198354 0.0099581757            0            0 
    3000    75.188527    -3688.256   -425.02228    14.567977   0.98632724       99  0.030546787 0.0049111089            0            0 
    4000    75.019396   -5669.3063   -427.69454    14.535207   0.98632724       99  0.019972039 0.0033375609            0            0 
    5000    90.415371   -2141.7596   -434.65925    17.518218   0.98632724       99  0.014909796  0.002514964            0            0 
    6000    78.212628   -943.75125   -428.80584    15.153904   0.98632724       99   0.01181521 0.0020316119            0            0 
    7000    71.754139   -2028.5122    -435.2139    13.902555   0.98632724       99 0.0099466198 0.0016755471            0            0 
    8000    84.446231   -1969.1657   -428.27313    16.361681   0.98632724       99 0.0084791272 0.0014442102            0            0 
    9000    70.952348   -2476.9812   -446.33824    14.170197    1.0162159      102 0.0077150892 0.0012556189            0            0 
   10000    71.418543   -1875.7083    -443.7214    14.263302    1.0162159      102 0.0068355714 0.0011197957            0            0 
   11000    86.094994   -4508.7581   -444.82687    17.194399    1.0162159      102 0.0061494515 0.0010082475            0            0 
   12000    81.906091   -1547.8105   -442.36719    16.357815    1.0162159      102 0.0055834729 0.00091775114            0            0 
   13000    57.221548   -4607.6222   -448.30939     11.42796    1.0162159      102 0.0051230355 0.00084046326            0            0 
   14000    61.288344   -2518.1779   -445.70636    12.240157    1.0162159      102 0.0047276997 0.00077602396            0            0 
   15000    85.787669   -2407.7111    -443.3834    17.133022    1.0162159      102 0.0043983485 0.00071920715            0            0 
   16000    74.845939   -3288.3403    -445.8247    14.947802    1.0162159      102 0.0042321884 0.00080654918            0            0 
   17000    73.835431   -1926.9566   -445.67476    14.745989    1.0162159      102 0.0039751059 0.00075470749            0            0 
   18000    72.634985    -3997.552    -447.2351    14.506243    1.0162159      102 0.0037395847 0.00071063946            0            0 
   19000    96.776472   -714.44132   -453.65552    19.904587    1.0461046      105 0.0036487876 0.00066993446            0            0 
   20000    75.470786    183.16972   -464.04688    15.522521    1.0461046      105 0.0034630763 0.00063350614            0            0 
   21000    65.658309   -773.41266   -466.27068    13.504331    1.0461046      105  0.003289113 0.00060198052            0            0 
Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms

Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.7882     | 10.264     | 14.758     |  93.2 | 10.93
Bond    | 0.028286   | 0.034218   | 0.039038   |   2.5 |  0.04
Kspace  | 0.57255    | 5.2227     | 8.8493     | 133.8 |  5.56
Neigh   | 0.3635     | 0.36915    | 0.37473    |   0.9 |  0.39
Comm    | 2.9961     | 3.2542     | 3.509      |  11.4 |  3.47
Output  | 0.0011675  | 0.0012342  | 0.001375   |   0.2 |  0.00
Modify  | 74.428     | 74.499     | 74.571     |   0.7 | 79.35
Other   |            | 0.2411     |            |       |  0.26

Nlocal:    26.25 ave 31 max 22 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost:    6049.25 ave 6133 max 5962 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:    23613 ave 35083 max 14025 min
Histogram: 1 0 0 1 1 0 0 0 0 1

Total # of neighbors = 94452
Ave neighs/atom = 899.543
Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0

Total wall time: 0:01:34
