LAMMPS (27 May 2021)
  using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - rigid box particles

units           lj
atom_style      sphere
atom_modify     map array first big
dimension       2

# read in clusters of rigid bodies

fix             molprop all property/atom mol ghost yes
read_data       data.box fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  420 atoms
  read_data CPU = 0.009 seconds

set             type 1 mass 1.0
Setting atom values ...
  420 settings made for mass
group           big type 1
420 atoms in group big
velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      soft 1.12
pair_coeff      1 1 0.0
pair_coeff      2 2 0.0 0.0
pair_coeff      1 2 0.0 0.0

variable        prefactor equal ramp(0,60)
fix             soft all adapt 1 pair soft a * * v_prefactor

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 big rigid molecule
  30 rigid bodies with 420 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.box.equil

compute         tbig all temp/sphere
thermo_modify   temp tbig

thermo          100
run             1000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 54 54 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, 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) = 5.557 | 5.557 | 5.558 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1.4252596            0            0   0.14931291    -8.727261 
     100    4.7699234    3.4203218            0    3.9200281   0.63667047 
     200    14.850064    5.3315601            0    6.8872811   0.71533738 
     300    21.249889    7.2094878            0    9.4356667    1.0710181 
     400    24.551027    9.2008598            0    11.772872    1.0133205 
     500    23.999755    11.562353            0    14.076613    1.3275867 
     600    25.022182    13.731564            0    16.352935    1.0236907 
     700    26.601942    15.850142            0    18.637012   0.80166569 
     800    24.154216    18.395444            0    20.925886    1.7521839 
     900      27.3897      20.3322            0    23.201597   0.65472411 
    1000    27.381112    22.600716            0    25.469214   0.69152692 
Loop time of 0.102477 on 4 procs for 1000 steps with 420 atoms

Performance: 4215597.184 tau/day, 9758.327 timesteps/s
87.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0086884  | 0.011084   | 0.012345   |   1.4 | 10.82
Neigh   | 0.0038968  | 0.0042393  | 0.0045272  |   0.4 |  4.14
Comm    | 0.028577   | 0.030455   | 0.032476   |   1.0 | 29.72
Output  | 0.00028127 | 0.00044494 | 0.0009265  |   0.0 |  0.43
Modify  | 0.041755   | 0.042937   | 0.044332   |   0.4 | 41.90
Other   |            | 0.01332    |            |       | 13.00

Nlocal:        105.000 ave         130 max          77 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:        39.0000 ave          49 max          21 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs:        140.500 ave         180 max         105 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 562
Ave neighs/atom = 1.3380952
Neighbor list builds = 158
Dangerous builds = 0

#undump         1
unfix           soft
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 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms    2 region plane
Created 124609 atoms
  create_atoms CPU = 0.025 seconds

set             type 2 mass 0.1
Setting atom values ...
  124609 settings made for mass
group           small type 2
124609 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 1.0

delete_atoms    overlap 1.0 small big
System init for delete_atoms ...
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 = 28 28 1
  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:308)
Deleted 51030 atoms, new total = 73999

# 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 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 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 rigid molecule
  30 rigid bodies with 420 atoms
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
fix             3 all enforce2d

# diagnostics

uncompute       tbig
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] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689)

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483)
thermo          1000

#dump           1 all atom 1000 dump.box

#dump           1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2

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 =  {P.{\,}J.~in{\,}'t~Veld 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 = {Comp.~Phys.~Comm.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Stratford2018,
 author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},
 title = {Implementation of multi-level contact detection in LAMMPS},
 year = {2018}
}

@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}
}

- fix srd command:

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

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

SRD info:
  SRD/big particles = 73579 420
  big particle diameter max/min = 1.0000000 1.0000000
  SRD temperature & lamda = 1.0000000 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 153 153 1
  SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000
  SRD per actual grid cell = 4.0557326
  SRD viscosity = 0.22929663
  big/SRD mass density ratio = 0.19661407
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.1966772 7.7276214
  ave/max big velocity = 2.1275716 5.8359099
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 = 38.289379, 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/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 27.16 | 27.18 | 27.21 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] f_2[12] 
       0    27.381112            0   0.25599398    42.234595    45.103092   0.74047865            0            0            0            0            0            0            0            0            0            0            0            0 
    1000    2.4803865        16183   0.24097572    42.197203    42.457053    10.685486        10313           34           34            0         1010        70756        23409        16183   0.91088084            0           10            0 
    2000    1.5192587        16288    0.2403558     42.18867     42.34783    12.991827        10247           51           51            0         1780        70756        23409        16288   0.91423542            0           10            0 
    3000    1.3453745        16254   0.24021083    42.181344    42.322288    10.311263         9901           36           36            0         2457        70756        23409        16254   0.92345925            0           10            0 
    4000    1.5208981        16348   0.24035467    42.188298    42.347631    11.118817        10195           32           33            2         3117        70756        23409        16348   0.93218296            0           10            0 
    5000    1.0700659        16291    0.2400755    42.186343    42.298445    9.3784033        10271           35           35            0         3810        70756        23409        16291   0.93211425            0           10            0 
    6000    1.0488908        16303    0.2400744    42.188368    42.298252    12.777782        10058           50           50            0         4557        70756        23409        16303   0.94151194            0           10            0 
    7000     1.331013        16244   0.24024721    42.189259    42.328698    10.953939        10388           36           36            0         5276        70756        23409        16244   0.94703063            0           10            0 
    8000   0.94738473        16321   0.23996282    42.179342    42.278592    11.767946        10161           41           41            0         5967        70756        23409        16321   0.94682195            0           10            0 
    9000    1.1009209        16291   0.24002765     42.17468    42.290015     8.045595        10584           33           33            0         6751        70756        23409        16291   0.94001295            0           10            0 
   10000    1.0564033        16282   0.23992848    42.161871    42.272542    12.284202        10257           40           40            0         7488        70756        23409        16282   0.94873736            0           10            0 
Loop time of 30.6515 on 4 procs for 10000 steps with 73999 atoms

Performance: 28187.845 tau/day, 326.248 timesteps/s
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.14666    | 0.20404    | 0.29182    |  13.1 |  0.67
Neigh   | 0.040061   | 0.050996   | 0.068192   |   4.8 |  0.17
Comm    | 1.087      | 1.2248     | 1.2747     |   7.2 |  4.00
Output  | 0.0024737  | 0.0037751  | 0.0060755  |   2.4 |  0.01
Modify  | 28.133     | 28.273     | 28.452     |   2.3 | 92.24
Other   |            | 0.8951     |            |       |  2.92

Nlocal:        18499.8 ave       20267 max       16093 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost:        74.5000 ave          90 max          57 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs:        590.250 ave         907 max         422 min
Histogram: 2 0 0 1 0 0 0 0 0 1

Total # of neighbors = 2361
Ave neighs/atom = 0.031905837
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:32
