LAMMPS (24 Oct 2018)
dimension       3
units           micro
atom_style      meso

variable        a equal 0.1             # lattice spacing         micrometers
variable        L equal $a*10
variable        L equal 0.1*10
variable        T equal 300.
variable        kB equal 1.3806504e-8   # picogram-micrometer^2/(microsecond^2-Kelvin)
variable        rho_0 equal 1.          # density                   picograms/micrometer^3
variable        c_0 equal 10.           # speed of sound            micrometers/microsecond
variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
variable        h equal $a*4.0          # kernel function cutoff    micrometers
variable        h equal 0.1*4.0          
variable        mass equal $a*$a*$a*${rho_0}
variable        mass equal 0.1*$a*$a*${rho_0}
variable        mass equal 0.1*0.1*$a*${rho_0}
variable        mass equal 0.1*0.1*0.1*${rho_0}
variable        mass equal 0.1*0.1*0.1*1
variable        dt equal 5e-4           # timestep                  microseconds
variable        skin equal 0.1*$h
variable        skin equal 0.1*0.4

region          box block -$L $L -$L $L -$L $L units box
region          box block -1 $L -$L $L -$L $L units box
region          box block -1 1 -$L $L -$L $L units box
region          box block -1 1 -1 $L -$L $L units box
region          box block -1 1 -1 1 -$L $L units box
region          box block -1 1 -1 1 -1 $L units box
region          box block -1 1 -1 1 -1 1 units box
create_box      1 box
Created orthogonal box = (-1 -1 -1) to (1 1 1)
  1 by 1 by 1 MPI processor grid
lattice         sc $a
lattice         sc 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1

create_atoms    1 box
Created 8000 atoms
  Time spent = 0.00285411 secs

mass            * ${mass}
mass            * 0.001
set             group all meso/rho ${rho_0}
set             group all meso/rho 1
  8000 settings made for meso/rho

pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
pair_style      sdpd/taitwater/isothermal 300 1 76787    
pair_coeff      * * ${rho_0} ${c_0} ${h}
pair_coeff      * * 1 ${c_0} ${h}
pair_coeff      * * 1 10 ${h}
pair_coeff      * * 1 10 0.4

variable        vx_sq atom vx*vx
variable        vy_sq atom vy*vy
variable        vz_sq atom vz*vz
compute         v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
variable        vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
variable        vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
variable        vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
variable        vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
variable        vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
variable        vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300

fix             1 all meso

neighbor        ${skin} bin
neighbor        0.04 bin
timestep        ${dt}
timestep        0.0005

thermo          10
thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check

run             200
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 0.44
  ghost atom cutoff = 0.44
  binsize = 0.22, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair sdpd/taitwater/isothermal, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check 
       0            0            0            0            0 
      10        0.005   0.70973271   0.71495693   0.71910087 
      20         0.01   0.90418096   0.88845437   0.89659567 
      30        0.015    0.9590736   0.97880338    0.9619016 
      40         0.02   0.98533774   0.96057682   0.95600448 
      50        0.025   0.96433662   0.96650071   0.95509683 
      60         0.03   0.96598029   0.96373656   0.96734888 
      70        0.035   0.95433045   0.98004764   0.96255924 
      80         0.04   0.97872906   0.95987289   0.96623598 
      90        0.045   0.99913888   0.99255731   0.95616142 
     100         0.05   0.98872675   0.97141018   0.95338841 
     110        0.055   0.97794592   0.97389258   0.98473719 
     120         0.06   0.98389266   0.96716284   0.95504862 
     130        0.065   0.98572886   0.96680923   0.95599065 
     140         0.07   0.97602684   0.97580081    0.9886878 
     150        0.075   0.99172003   0.95027467   0.96028033 
     160         0.08   0.96793247   0.94590928   0.95644301 
     170        0.085   0.94167619   0.98048861   0.93439426 
     180         0.09   0.97277934   0.97383622   0.96900866 
     190        0.095   0.96647288    1.0027643   0.96230782 
     200          0.1   0.94864291   0.95902585   0.96398175 
Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms

Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 59.92      | 59.92      | 59.92      |   0.0 | 99.68
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.11154    | 0.11154    | 0.11154    |   0.0 |  0.19
Output  | 0.0063498  | 0.0063498  | 0.0063498  |   0.0 |  0.01
Modify  | 0.043546   | 0.043546   | 0.043546   |   0.0 |  0.07
Other   |            | 0.02811    |            |       |  0.05

Nlocal:    8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    16389 ave 16389 max 16389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.456e+06 ave 1.456e+06 max 1.456e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1456000
Ave neighs/atom = 182
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00
