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 - rigid star 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.star fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  270 atoms
  read_data CPU = 0.011 seconds

set             type 1 mass 1.0
Setting atom values ...
  270 settings made for mass
group           big type 1
270 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 270 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.star.equil

compute         tbig all temp/sphere
thermo_modify   temp tbig

thermo          100
run             1000
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 = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 38 38 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) = 5.562 | 5.562 | 5.562 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.3101488      0              0              0.21350573     0.32876464   
       100   5.0954142      3.291475       0              4.1218387      1.0087565    
       200   13.041252      4.6176595      0              6.7429006      1.5291618    
       300   11.912727      7.0921814      0              9.0335147      1.9578844    
       400   17.60886       8.3666709      0              11.236263      1.602563     
       500   16.786375      10.630838      0              13.366396      1.7725508    
       600   18.470347      12.42157       0              15.431552      2.1627885    
       700   19.39794       14.349074      0              17.510219      1.9554238    
       800   19.082984      16.464746      0              19.574566      2.2424126    
       900   20.702091      18.253108      0              21.626782      1.8041661    
      1000   18.299191      20.699563      0              23.681654      2.9475408    
Loop time of 0.0585091 on 1 procs for 1000 steps with 270 atoms

Performance: 7383466.593 tau/day, 17091.358 timesteps/s, 4.615 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.017165   | 0.017165   | 0.017165   |   0.0 | 29.34
Neigh   | 0.0058479  | 0.0058479  | 0.0058479  |   0.0 |  9.99
Comm    | 0.0028221  | 0.0028221  | 0.0028221  |   0.0 |  4.82
Output  | 0.00017384 | 0.00017384 | 0.00017384 |   0.0 |  0.30
Modify  | 0.03015    | 0.03015    | 0.03015    |   0.0 | 51.53
Other   |            | 0.00235    |            |       |  4.02

Nlocal:            270 ave         270 max         270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             73 ave          73 max          73 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            418 ave         418 max         418 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
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 60025 atoms
  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
  create_atoms CPU = 0.013 seconds

set             type 2 mass 0.1
Setting atom values ...
  60025 settings made for mass
group           small type 2
60025 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 0.5

delete_atoms    overlap 0.5 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: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 19 19 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:312)
Deleted 16305 atoms, new total = 43990

# 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 270 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:904)

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.star

#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 =  {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 = 43720 270
  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: 106 106 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
  SRD per actual grid cell = 5.5586635
  SRD viscosity = 0.23558168
  big/SRD mass density ratio = 0.14409881
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 = 4.1908497 7.725824
  ave/max big velocity = 2.202625 5.4167964
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 = 26.586808, 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) = 41.29 | 41.29 | 41.29 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   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
      1000   1.2074332      8227           0.22959643     37.210444      37.407211      7.9007359      14317          47             47             0              649            28900          11236          8227           1.0260288      0              3              0            
      2000   1.2044605      8206           0.22945824     37.188414      37.384697      5.8738384      14470          63             63             0              1423           28900          11236          8206           1.018589       0              4              0            
      3000   1.1060368      8226           0.22936549     37.189341      37.369584      4.7013136      14255          51             51             0              2207           28900          11236          8226           1.0007203      0              4              0            
      4000   1.2395587      8236           0.2294891      37.187723      37.389725      5.7916781      14371          56             56             0              2916           28900          11236          8236           1.0229966      0              4              0            
      5000   1.3332555      8236           0.22962818     37.195112      37.412383      10.662157      14373          61             61             0              3740           28900          11236          8236           1.0094713      0              4              0            
      6000   1.2991744      8192           0.22957221     37.191547      37.403264      1.2016626      14145          56             58             0              4425           28900          11236          8192           1.0215234      0              4              0            
      7000   1.0110737      8147           0.22923336     37.18329       37.348057      6.2493424      14200          59             59             0              5102           28900          11236          8147           1.0163405      0              4              0            
      8000   0.79508387     8168           0.22908516     37.194343      37.323912      9.832591       14355          45             45             0              5839           28900          11236          8168           1.0063207      0              4              0            
      9000   1.0340542      8207           0.2292515      37.1825        37.351013      11.458942      14220          54             54             0              6606           28900          11236          8207           1.0074421      0              4              0            
     10000   0.96342976     8202           0.22912995     37.174206      37.33121       1.7523017      14308          53             53             0              7379           28900          11236          8202           1.0126923      0              4              0            
Loop time of 18.5504 on 1 procs for 10000 steps with 43990 atoms

Performance: 46575.737 tau/day, 539.071 timesteps/s, 23.714 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.21961    | 0.21961    | 0.21961    |   0.0 |  1.18
Neigh   | 0.055763   | 0.055763   | 0.055763   |   0.0 |  0.30
Comm    | 0.22073    | 0.22073    | 0.22073    |   0.0 |  1.19
Output  | 0.0013822  | 0.0013822  | 0.0013822  |   0.0 |  0.01
Modify  | 17.872     | 17.872     | 17.872     |   0.0 | 96.34
Other   |            | 0.1812     |            |       |  0.98

Nlocal:          43990 ave       43990 max       43990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            138 ave         138 max         138 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1587 ave        1587 max        1587 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1587
Ave neighs/atom = 0.036076381
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:20
