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 1 by 1 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) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          338   -4.1890564 9.2628112e-06     18.98377    739.06991 
     100          338   -30.182886   0.85607237   -6.1539961   -2535.3207 
Loop time of 0.0525794 on 1 procs for 100 steps with 24 atoms

99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
        -4.18904713252     -28.9258064504     -29.3268133965
  Force two-norm initial, final = 18.0027 42.4511
  Force max component initial, final = 5.8993 16.0523
  Final line search alpha, max atom move = 0.00353207 0.056698
  Iterations, force evaluations = 100 238

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.044199   | 0.044199   | 0.044199   |   0.0 | 84.06
Bond    | 0.00049019 | 0.00049019 | 0.00049019 |   0.0 |  0.93
Kspace  | 0.0031631  | 0.0031631  | 0.0031631  |   0.0 |  6.02
Neigh   | 0.00046444 | 0.00046444 | 0.00046444 |   0.0 |  0.88
Comm    | 0.0034101  | 0.0034101  | 0.0034101  |   0.0 |  6.49
Output  | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 |   0.0 |  0.04
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0008333  |            |       |  1.58

Nlocal:    24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2047 ave 2047 max 2047 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4936 ave 4936 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4936
Ave neighs/atom = 205.667
Ave special neighs/atom = 2
Neighbor list builds = 2
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) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    518.26667   -30.182886            0   -7.0100684     993.1985 
    1000     326.9865   -62.258445            0   -47.638175   -5.3440813 
Loop time of 0.14263 on 1 procs for 1000 steps with 24 atoms

Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.10849    | 0.10849    | 0.10849    |   0.0 | 76.07
Bond    | 0.00015426 | 0.00015426 | 0.00015426 |   0.0 |  0.11
Kspace  | 0.01205    | 0.01205    | 0.01205    |   0.0 |  8.45
Neigh   | 0.0046577  | 0.0046577  | 0.0046577  |   0.0 |  3.27
Comm    | 0.011531   | 0.011531   | 0.011531   |   0.0 |  8.08
Output  | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 |   0.0 |  0.01
Modify  | 0.0037699  | 0.0037699  | 0.0037699  |   0.0 |  2.64
Other   |            | 0.001957   |            |       |  1.37

Nlocal:    24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1660 ave 1660 max 1660 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5112 ave 5112 max 5112 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5112
Ave neighs/atom = 213
Ave special neighs/atom = 2
Neighbor list builds = 25
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) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
    1000     326.9865   -4.3509713   -62.258445     14.62027   0.23910963       24            0            0            0            0 
    2000    116.99793   -5344.1527   -286.61595    17.088682   0.74721761       75  0.048183096  0.013941446            0            0 
    3000    106.86746   -3920.4926   -361.60598    18.794545   0.89666113       90  0.035637919  0.012768883            0            0 
    4000    75.002668    540.46846    -414.8511    14.531966   0.98632724       99  0.025963651 0.0093451705            0            0 
    5000    79.924788   -2131.1173   -437.21216    15.962121    1.0162159      102  0.019879728 0.0070418993            0            0 
    6000    95.552773   -3647.0233   -438.24276    19.083253    1.0162159      102  0.015753613 0.0056885133            0            0 
    7000    79.501736   -2071.5369   -440.77351    15.877631    1.0162159      102   0.01326216 0.0046915318            0            0 
    8000    62.567091   -3102.9616   -442.21884    12.495541    1.0162159      102  0.011305503 0.0040437885            0            0 
    9000    68.324047   -3812.7866   -440.46835    13.645287    1.0162159      102 0.0099549538 0.0035157329            0            0 
   10000    83.857631   -2158.2659    -444.8183    16.747566    1.0162159      102 0.0088200922 0.0031354281            0            0 
   11000    68.350984   -2084.0789   -440.14081    13.650667    1.0162159      102 0.0081331455 0.0030247424            0            0 
   12000    76.867315   -1585.6723   -443.36199      15.3515    1.0162159      102 0.0073845932 0.0027532534            0            0 
   13000     59.74266   -2211.0211   -446.07791    11.931462    1.0162159      102 0.0067756276 0.0025213898            0            0 
   14000    81.154979    -907.0176   -441.53368    16.207808    1.0162159      102 0.0062527642 0.0023280719            0            0 
   15000    66.814346   -2804.5134   -455.80704      13.7421    1.0461046      105 0.0059590528 0.0021576214            0            0 
   16000     71.42983   -3930.4004   -458.43218    14.691394    1.0461046      105 0.0055547473 0.0020163729            0            0 
   17000    89.624855   -3569.8136   -455.18164    18.433672    1.0461046      105 0.0052173265 0.0018867687            0            0 
   18000    63.519962   -1882.8157   -456.58939    13.064525    1.0461046      105 0.0049082049 0.0017765986            0            0 
   19000    71.872698   -2243.5046   -454.93359    14.782481    1.0461046      105 0.0046439115 0.0016748361            0            0 
   20000    73.660765   -2285.3173   -476.35473    15.589381    1.0759934      108 0.0045124933 0.0015837653            0            0 
   21000    95.675868    987.92089   -475.46736    20.248603    1.0759934      108  0.004285814 0.0015049513            0            0 
Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms

Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 38.053     | 38.053     | 38.053     |   0.0 | 16.83
Bond    | 0.089673   | 0.089673   | 0.089673   |   0.0 |  0.04
Kspace  | 0.92778    | 0.92778    | 0.92778    |   0.0 |  0.41
Neigh   | 1.2619     | 1.2619     | 1.2619     |   0.0 |  0.56
Comm    | 0.97483    | 0.97483    | 0.97483    |   0.0 |  0.43
Output  | 0.0013306  | 0.0013306  | 0.0013306  |   0.0 |  0.00
Modify  | 184.68     | 184.68     | 184.68     |   0.0 | 81.66
Other   |            | 0.171      |            |       |  0.08

Nlocal:    108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7850 ave 7850 max 7850 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    99828 ave 99828 max 99828 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 99828
Ave neighs/atom = 924.333
Ave special neighs/atom = 2
Neighbor list builds = 20439
Dangerous builds = 0

Total wall time: 0:03:46
