LAMMPS (11 Aug 2017)
########################################################################
### Pure diffusion with a reaction source term analog of a periodic  ###
### Poiseuille flow problem using transport DPD (tDPD) simulation    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### tDPD system setup follows Fig.1 in the publication:              ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis.          ###
### "Transport dissipative particle dynamics model for mesoscopic    ###
### advection-diffusion-reaction problems. J. Chem. Phys.,           ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254                        ###
########################################################################
units 		        lj
dimension	        3
boundary	        p p p
neighbor	        0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style	        tdpd 2

region     tdpd     block -10 10 -10 10 -5 5 units box
create_box          1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
  1 by 1 by 1 MPI processor grid
create_atoms        1 random 16000 276438 NULL
Created 16000 atoms
mass                1 1.0
set                 atom * cc 1 1.0
  16000 settings made for cc index 1
set                 atom * cc 2 1.0
  16000 settings made for cc index 2

pair_style          tdpd 1.0 1.58 9872598
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0

compute             mythermo all temp
thermo              50
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

fix         mvv     all mvv/tdpd 0.5
fix         upper1  all tdpd/source 1 cuboid 0.0  5.0 0.0 20.0 10.0 10.0  0.01
fix         lower1  all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix         upper2  all tdpd/source 2 cuboid 0.0  5.0 0.0 20.0 10.0 10.0 -0.01
fix         lower2  all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0  0.01

timestep            0.01
run                 500
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.78
  ghost atom cutoff = 1.78
  binsize = 0.89, bins = 23 23 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair tdpd, 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) = 11.3 | 11.3 | 11.3 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            1    48.948932            0    50.448838    202.19166 
      50   0.99837766    43.949877            0    45.447349    195.80936 
     100   0.99846831    43.756995            0    45.254604    198.22348 
     150    1.0026903     43.72408            0    45.228021    196.61676 
     200    1.0063144    43.722388            0    45.231765    194.17954 
     250    1.0032304    43.721864            0    45.226615    197.85829 
     300    0.9932656    43.703526            0    45.193331    196.57406 
     350    1.0002916    43.720498            0    45.220841    193.55346 
     400   0.99475486    43.722965            0    45.215004    196.81546 
     450    1.0011803    43.712447            0    45.214124    200.46118 
     500    1.0009006    43.708984            0    45.210241    197.38953 
Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms

Performance: 4498.474 tau/day, 5.207 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 90.083     | 90.083     | 90.083     |   0.0 | 93.80
Neigh   | 5.049      | 5.049      | 5.049      |   0.0 |  5.26
Comm    | 0.34141    | 0.34141    | 0.34141    |   0.0 |  0.36
Output  | 0.00092816 | 0.00092816 | 0.00092816 |   0.0 |  0.00
Modify  | 0.45991    | 0.45991    | 0.45991    |   0.0 |  0.48
Other   |            | 0.09865    |            |       |  0.10

Nlocal:    16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    749379 ave 749379 max 749379 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749379
Ave neighs/atom = 46.8362
Neighbor list builds = 183
Dangerous builds = 0
reset_timestep      0

compute     cc1     all tdpd/cc/atom 1
compute     cc2     all tdpd/cc/atom 2
compute     bin     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile

run                 100
Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1.0009006    43.708984            0    45.210241     199.3205 
      50    1.0007276    43.704844            0    45.205842    197.77053 
     100    1.0039032    43.714201            0    45.219961    197.31118 
Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms

Performance: 4539.577 tau/day, 5.254 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 17.842     | 17.842     | 17.842     |   0.0 | 93.74
Neigh   | 0.98674    | 0.98674    | 0.98674    |   0.0 |  5.18
Comm    | 0.066013   | 0.066013   | 0.066013   |   0.0 |  0.35
Output  | 0.00016284 | 0.00016284 | 0.00016284 |   0.0 |  0.00
Modify  | 0.11795    | 0.11795    | 0.11795    |   0.0 |  0.62
Other   |            | 0.02012    |            |       |  0.11

Nlocal:    16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    14126 ave 14126 max 14126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    748927 ave 748927 max 748927 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 748927
Ave neighs/atom = 46.8079
Neighbor list builds = 37
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:01:55
