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 - ellipsoids

units           lj
atom_style      ellipsoid
atom_modify     first big
dimension       2

# create big ellipsoidal particles

lattice         sq 0.14
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
region          box block 0 10 0 10 -0.5 0.5
create_box      2 box
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
  2 by 2 by 1 MPI processor grid
create_atoms    1 region box
Created 100 atoms
  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
  create_atoms CPU = 0.001 seconds

set             type 1 mass 1.0
Setting atom values ...
  100 settings made for mass
set             type 1 shape 3.0 1.0 1.0
Setting atom values ...
  100 settings made for shape
group           big type 1
100 atoms in group big
set             group big quat/random 29898
Setting atom values ...
  100 settings made for quat/random

velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      gayberne 1.0 3.0 1.0 4.0
pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 big nve/asphere
fix             2 all enforce2d

compute         rot big temp/asphere
compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez

#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez

thermo_style    custom step temp c_rot epair etotal press
thermo          100

run             1000

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

Your simulation uses code contributions which should be cited:

- pair gayberne command: doi:10.1063/1.3058435

@Article{Brown09,
 author =  {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
 title =   {Liquid Crystal Nanodroplets in Solution},
 journal = {J.~Chem.\ Phys.},
 year =    2009,
 volume =  130,
 number =  4,
 pages =   {044901}
}

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

Generated 0 of 1 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 = 4.3
  ghost atom cutoff = 4.3
  binsize = 2.15, bins = 13 13 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair gayberne, 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) = 4.61 | 4.61 | 4.61 Mbytes
   Step          Temp          c_rot          E_pair         TotEng         Press     
         0   1.44           0.95677852     2.7038078      4.1294078      10.518912    
       100   2.5524145      2.801098      -0.37027046     2.1566199      0.84703874   
       200   2.6266386      2.7938164     -0.35322565     2.2471465      1.004886     
       300   2.9987557      2.9499545     -0.58917376     2.3795944      0.73081788   
       400   2.8557446      2.8208128     -0.39904801     2.4281391      0.91808964   
       500   2.4399047      2.8255746     -0.40056447     2.0149412      1.0538908    
       600   2.854258       2.9166789     -0.53424483     2.2914706      0.8117508    
       700   2.9593679      2.8231211     -0.40051715     2.5292571      1.1630889    
       800   2.7632972      2.9060855     -0.52075354     2.2149107      0.77106773   
       900   2.9905599      2.8869667     -0.49099386     2.4696604      0.69616823   
      1000   2.8470131      2.9005016     -0.51282147     2.3057215      0.68817329   
Loop time of 0.0666302 on 4 procs for 1000 steps with 100 atoms

Performance: 6483542.632 tau/day, 15008.201 timesteps/s, 1.501 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.039208   | 0.042833   | 0.045871   |   1.2 | 64.29
Neigh   | 0.00065929 | 0.00071982 | 0.00076852 |   0.0 |  1.08
Comm    | 0.013998   | 0.017169   | 0.02087    |   1.9 | 25.77
Output  | 0.00018817 | 0.00020663 | 0.00025962 |   0.0 |  0.31
Modify  | 0.0035046  | 0.0035933  | 0.003701   |   0.1 |  5.39
Other   |            | 0.002109   |            |       |  3.16

Nlocal:             25 ave          27 max          24 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost:          42.25 ave          45 max          38 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs:          92.25 ave         104 max          85 min
Histogram: 1 0 1 1 0 0 0 0 0 1

Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
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 120.0
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
create_atoms    2 region plane
Created 85849 atoms
  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
  create_atoms CPU = 0.004 seconds

set             type 2 mass 0.01
Setting atom values ...
  85849 settings made for mass
group           small type 2
85849 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 2.0

neigh_modify    one 10000

delete_atoms    overlap 1.6 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 10000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 20 20 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 71060 atoms, new total = 14889

# 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      gayberne 1.0 3.0 1.0 4.0
pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 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        0.0005

fix             1 big nve/asphere
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   collision noslip search 0.2 inside ignore exact no bounce 50
fix             3 all enforce2d

# diagnostics

compute         tbig big temp/asphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp c_rot f_2[9] 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]

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

#dump           1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez

#dump           2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    2 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 =  {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 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 14789 100
  big particle diameter max/min = 3 1
  SRD temperature & lamda = 1 0.1
  SRD max distance & max velocity = 0.4 40
  SRD grid counts: 107 107 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
  SRD per actual grid cell = 1.9275711
  SRD viscosity = 0.68810145
  big/SRD mass density ratio = 1.3736715
  # of rescaled SRD velocities = 0
  ave/max small velocity = 13.30933 24.335888
  ave/max big velocity = 2.080284 5.0567191
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 10000, page size: 100000
  master list distance cutoff = 4.3
  ghost atom cutoff = 4.3
  binsize = 26.726124, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair gayberne, 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) = 16.89 | 16.9 | 16.91 Mbytes
   Step          Temp          c_rot          f_2[9]         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   2.9005016      2.9005016      0              0.025582147   -0.51282147     3.8089259      0.89862191     0              0              0              0              0              0              0              0              0              0              0              0            
      1000   2.7138279      2.7138279      0.82437872     0.023781703   -0.50274582     3.5408578      1.6816604      13758          32             34             0              274            66564          11449          4238           0.82437872     24             50             0            
      2000   1.3183118      1.3183118      0.91362053     0.0077748292  -0.80669023     1.1575943      1.1678425      14118          23             23             0              414            66564          11449          4269           0.91362053     24             50             0            
      3000   1.3117991      1.3117991      0.96889539     0.0065133847  -0.98480276     0.96977785     0.51801823     14675          35             36             0              588            66564          11449          4291           0.96889539     26             50             0            
      4000   1.1034132      1.1034132      0.95899765     0.0042496304  -1.0113582      0.63272747     0.6382343      15146          38             38             0              776            66564          11449          4309           0.95899765     26             50             0            
      5000   1.0814177      1.0814177      1.0037423      0.0047549676  -0.90334518     0.70796713     0.76138491     15275          40             40             0              973            66564          11449          4285           1.0037423      26             50             0            
      6000   1.0515425      1.0515425      0.98728204     0.0041039749  -0.95575757     0.61104083     0.61253791     15685          34             34             0              1205           66564          11449          4328           0.98728204     26             50             0            
      7000   0.96229389     0.96229389     1.0146054      0.0031968892  -0.95783307     0.47598483     0.4469161      15944          43             43             0              1412           66564          11449          4391           1.0146054      27             50             0            
      8000   0.98798058     0.98798058     0.99692702     0.0037348841  -0.91600418     0.55608689     0.50558822     16250          43             43             0              1637           66564          11449          4330           0.99692702     27             50             0            
      9000   1.0120554      1.0120554      1.0099521      0.0039518454  -0.91957229     0.58839026     0.4092229      16367          43             44             0              1899           66564          11449          4309           1.0099521      27             50             0            
     10000   1.104152       1.104152       0.9993147      0.0053713858  -0.84544079     0.79974564     0.5119979      16331          50             50             0              2108           66564          11449          4353           0.9993147      27             50             0            
Loop time of 2.95619 on 4 procs for 10000 steps with 14889 atoms

Performance: 146134.205 tau/day, 3382.736 timesteps/s, 50.366 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48773    | 0.52727    | 0.62879    |   8.1 | 17.84
Neigh   | 0.0070094  | 0.0072204  | 0.0076255  |   0.3 |  0.24
Comm    | 0.12898    | 0.22553    | 0.265      |  11.8 |  7.63
Output  | 0.0005957  | 0.00064777 | 0.00075264 |   0.0 |  0.02
Modify  | 2.1317     | 2.1512     | 2.166      |   0.9 | 72.77
Other   |            | 0.04427    |            |       |  1.50

Nlocal:        3722.25 ave        3968 max        3389 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost:          39.75 ave          44 max          35 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:            101 ave         125 max          86 min
Histogram: 1 0 1 1 0 0 0 0 0 1

Total # of neighbors = 404
Ave neighs/atom = 0.027134126
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:03
