LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - poydisperse spheres

units           lj
atom_style      sphere
atom_modify     first big
dimension       2

# create big particles with 3 different types and diameters

lattice         sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region          box block 0 10 0 10 -0.5 0.5
create_box      4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  1 by 1 by 1 MPI processor grid
create_atoms    1 region box
Created 100 atoms
  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  create_atoms CPU = 0.000 seconds

group           big type 1
100 atoms in group big
set             group big type/fraction 2 0.33 394895
Setting atom values ...
  35 settings made for type/fraction
set             group big type/fraction 3 0.5 989894
Setting atom values ...
  57 settings made for type/fraction
group           big type 2 3
100 atoms in group big

set             type 1*3 mass 1.0
Setting atom values ...
  100 settings made for mass
velocity        big create 1.44 87287 loop geom

# equilibrate big particles, repulsive only to prevent aggregation

pair_style      lj/cut 1.12
pair_coeff      1 1 1.0 1.0 1.12
pair_coeff      2 2 1.0 2.0 2.24
pair_coeff      3 3 1.0 1.5 1.68
pair_coeff      4 4 0.0 1.0 0.0

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 big nve
fix             2 all enforce2d

#dump           1 all atom 10 dump.poly.equil

run             1000
Generated 6 of 6 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 = 2.54
  ghost atom cutoff = 2.54
  binsize = 1.27, bins = 15 15 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.44          -0.16013916     0              1.2654608      1.1298975    
      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
Loop time of 0.00622873 on 1 procs for 1000 steps with 100 atoms

Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0015709  | 0.0015709  | 0.0015709  |   0.0 | 25.22
Neigh   | 0.0014016  | 0.0014016  | 0.0014016  |   0.0 | 22.50
Comm    | 0.0012066  | 0.0012066  | 0.0012066  |   0.0 | 19.37
Output  | 6.169e-06  | 6.169e-06  | 6.169e-06  |   0.0 |  0.10
Modify  | 0.0013508  | 0.0013508  | 0.0013508  |   0.0 | 21.69
Other   |            | 0.0006926  |            |       | 11.12

Nlocal:            100 ave         100 max         100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             60 ave          60 max          60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            152 ave         152 max         152 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0

#undump         1
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms    4 region plane
Created 83521 atoms
  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  create_atoms CPU = 0.016 seconds

set             type 4 mass 0.1
Setting atom values ...
  83521 settings made for mass
group           small type 4
83521 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set *-4 cutoffs to non-zero values

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 1.0 2.0
pair_coeff      3 3 1.0 1.5
pair_coeff      1 4 0.0 1.0 0.5
pair_coeff      2 4 0.0 1.0 1.0
pair_coeff      3 4 0.0 1.0 0.75
pair_coeff      4 4 0.0 1.0 0.0

delete_atoms    overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 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 = 14 14 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 1.12
pair_coeff      1 1 1.0 1.0 1.12
pair_coeff      2 2 1.0 2.0 2.24
pair_coeff      3 3 1.0 1.5 1.68
pair_coeff      4 4 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big nve
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
fix             3 all enforce2d

# diagnostics

compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 1000 dump.poly

#dump           1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 20111 100
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 73 73 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
  SRD per actual grid cell = 4.9371727
  SRD viscosity = 0.23321983
  big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.1934421 7.74495
  ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.54
  ghost atom cutoff = 2.54
  binsize = 18.257419, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]    
         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
      1000   1.0181191      3924           0.0076572255   0.030604433    1.5476019      3.7992573      7242           26             26             0              635            15876          5329           3924           0.98110339     0              3            
      2000   0.69783736     3992           0.0027817464  -0.47755891     0.56221876     1.9887267      7740           34             34             1              1186           15876          5329           3992           1.0611575      0              24           
      3000   0.89084297     3981           0.004323119   -0.45361044     0.87374558     1.7342893      7775           24             24             0              1923           15876          5329           3981           1.1207371      0              24           
      4000   0.84391846     4036           0.0045581483  -0.33619115     0.92124735     1.8456288      8060           43             43             0              2734           15876          5329           4036           1.1481354      0              24           
      5000   0.69548234     4056           0.0030033315  -0.42926535     0.60700333     1.6113509      8260           33             33             0              3638           15876          5329           4056           1.148749       0              24           
      6000   0.71729125     4023           0.0035318938  -0.35493291     0.71383106     1.673491       8224           29             29             0              4528           15876          5329           4023           1.1602572      0              24           
      7000   0.90145513     4032           0.0047423524  -0.38469129     0.95847685     1.7537778      8382           31             31             0              5395           15876          5329           4032           1.1543513      0              24           
      8000   0.6739295      4026           0.0029910322  -0.39963744     0.60451751     1.646528       8409           35             35             0              6293           15876          5329           4026           1.1540519      0              24           
      9000   0.80563959     4041           0.0042947965  -0.33238166     0.86802133     1.6597032      8429           29             29             0              7164           15876          5329           4041           1.1880521      0              24           
     10000   0.90407954     4022           0.0046865656  -0.39987673     0.94720178     1.445708       8349           30             30             0              8189           15876          5329           4022           1.171667       0              24           
Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms

Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.019832   | 0.019832   | 0.019832   |   0.0 |  0.35
Neigh   | 0.020738   | 0.020738   | 0.020738   |   0.0 |  0.37
Comm    | 0.056875   | 0.056875   | 0.056875   |   0.0 |  1.01
Output  | 0.00083247 | 0.00083247 | 0.00083247 |   0.0 |  0.01
Modify  | 5.4828     | 5.4828     | 5.4828     |   0.0 | 97.05
Other   |            | 0.06854    |            |       |  1.21

Nlocal:          20211 ave       20211 max       20211 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             49 ave          49 max          49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            160 ave         160 max         160 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 160
Ave neighs/atom = 0.0079164811
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:11
