LAMMPS (17 Feb 2022)
# GCMC for CO2 molecular fluid, rigid/small dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].

# 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
molecule        co2mol CO2.txt
Read molecule template co2mol:
  1 molecules
  0 fragments
  3 atoms with max type 2
  2 bonds with max type 1
  1 angles with max type 1
  0 dihedrals with max type 0
  0 impropers with max type 0
create_atoms    0 box mol co2mol 464563 units box
Created 24 atoms
  using box units in orthogonal box = (0 0 0) to (10 10 10)
  create_atoms CPU = 0.002 seconds

# rigid CO2 TraPPE model

pair_coeff      1   1  0.053649   2.8
pair_coeff      2   2  0.156973   3.05
bond_coeff      1       0       1.16
angle_coeff     1       0       180

# masses

mass 1 12.0107
mass 2 15.9994

# MD settings

group           co2 type 1 2
24 atoms in group co2
neighbor        2.0 bin
neigh_modify    every 1 delay 10 check yes
velocity        all create ${temp} 54654
velocity        all create 338.0 54654
timestep        1.0

# rigid constraints with thermostat

fix             myrigid co2 rigid/small molecule mol co2mol
  create bodies CPU = 0.000 seconds
  8 rigid bodies with 24 atoms
  1.16 = max distance from body owner to body atom

# dynamically update  fix rigid/nvt/small temperature ndof
fix_modify      myrigid dynamic/dof yes

# gcmc

variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid

# atom counts

variable        carbon atom "type==1"
variable        oxygen atom "type==2"
group           carbon dynamic co2 var carbon
dynamic group carbon defined
group           oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable        nC equal count(carbon)
variable        nO equal count(oxygen)

# 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)

# dynamically update default temperature ndof
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 v_nC v_nO
thermo          1000

# run

run             20000
Ewald initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
  G vector (1/distance) = 0.16463644
  estimated absolute RMS force accuracy = 0.033206372
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
  generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:486)
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 (src/neighbor.cpp:635)
Neighbor list info ...
  update every 1 steps, delay 10 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
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.98 | 15.98 | 15.98 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
       0    386.52184    23582.465   -3.2433417    14.209828    0.5846359       24            0            0            0            0            8           16 
    1000    384.36044    168.85423    -23.23758    19.858894   0.80387436       33  0.066251757  0.059749054            0            0           11           22 
    2000    259.20275    79.927114   -7.8419025    6.9537074   0.43847693       18  0.051929539  0.052057755            0            0            6           12 
    3000    302.33017    445.51546   -13.370306    12.616643   0.65771539       27  0.047267159  0.046725853            0            0            9           18 
    4000    311.19874   -941.64049   -29.224589    17.624862   0.87695385       36  0.054172258  0.052814245            0            0           12           24 
    5000    357.15913    -643.8797   -23.716174    18.453474   0.80387436       33  0.044110118  0.044289139            0            0           11           22 
    6000    343.81577    816.03183   -23.966196    17.764058   0.80387436       33  0.042107357  0.041553567            0            0           11           22 
    7000    360.66228   -396.06153   -12.261373    13.259144    0.5846359       24  0.046352562  0.047370093            0            0            8           16 
    8000    536.38773    97.164555   -1.3308134    6.3954798   0.21923846        9  0.088510977  0.090746839            0            0            3            6 
    9000     768.3631    251.53458  -0.87836731    5.3441371   0.14615898        6   0.11093712   0.11396968            0            0            2            4 
   10000    219.20608   -312.87929   -18.365974    9.1477634   0.65771539       27     0.117446   0.11875767            0            0            9           18 
   11000    380.32873    -455.7618   -19.955783    17.761107   0.73079488       30   0.11798452   0.11947738            0            0           10           20 
   12000    379.24355     197.4359   -2.1821544     4.521812   0.21923846        9   0.12913146   0.13205423            0            0            3            6 
   13000    396.07556    137.32879   -13.038496    14.561054    0.5846359       24   0.14552187   0.14709749            0            0            8           16 
   14000    324.11748     156.7682   -7.5905299    8.6951939   0.43847693       18   0.14458311   0.14598959            0            0            6           12 
   15000    355.07055   -171.07765   -14.067188     14.81757   0.65771539       27   0.14061899   0.14191715            0            0            9           18 
   16000    303.99764   -48.184319    -22.94389     15.70676   0.80387436       33   0.13709205   0.13778218            0            0           11           22 
   17000     233.8048   -12.817441   -10.840623    8.5954415    0.5846359       24   0.13670252   0.13812514            0            0            8           16 
   18000    288.74916    157.63378   -6.0604526    7.7463575   0.43847693       18   0.14212703   0.14298282            0            0            6           12 
   19000    285.23652    -41.79006   -1.0403841    1.9838837   0.14615898        6    0.1500458   0.15058244            0            0            2            4 
   20000    537.62536    77.091199   -3.9443433    9.0811682   0.29231795       12   0.15563619    0.1561609            0            0            4            8 
Loop time of 8.33966 on 4 procs for 20000 steps with 12 atoms

Performance: 207.203 ns/day, 0.116 hours/ns, 2398.178 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.23792    | 0.33196    | 0.40407    |  10.7 |  3.98
Bond    | 0.0061255  | 0.0062467  | 0.0063458  |   0.1 |  0.07
Kspace  | 0.1676     | 0.2404     | 0.33413    |  12.6 |  2.88
Neigh   | 0.019046   | 0.019101   | 0.01916    |   0.0 |  0.23
Comm    | 0.67736    | 0.68025    | 0.68266    |   0.3 |  8.16
Output  | 0.00081757 | 0.00087737 | 0.0010462  |   0.0 |  0.01
Modify  | 7.0053     | 7.0093     | 7.0134     |   0.1 | 84.05
Other   |            | 0.05152    |            |       |  0.62

Nlocal:              3 ave           5 max           0 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost:            711 ave         750 max         671 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs:         321.25 ave         568 max           0 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 1285
Ave neighs/atom = 107.08333
Ave special neighs/atom = 2
Neighbor list builds = 20160
Dangerous builds = 0

Total wall time: 0:00:08
