LAMMPS (11 Aug 2017)
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### Heat conduction analog of periodic Poiseuille flow problem       ###
### using energy-conserving DPD (eDPD) simulation                    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### mDPD system setup follows Fig.12 in the publication:             ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis.      ###
### "Energy-conserving dissipative particle dynamics with            ###
### temperature-dependent properties". J. Comput. Phys.,             ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003               ###
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units 		        lj
dimension	        3
boundary	        p p p
neighbor	        0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style	        edpd

region     edpd     block -10 10 -10 10 -5 5 units box
create_box          1 edpd
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 * edpd/temp 1.0
  16000 settings made for edpd/temp
set                 atom * edpd/cv 1.0E5
  16000 settings made for edpd/cv

pair_style          edpd 1.58 9872598
#pair_coeff          1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58                         power 10.54 -3.66 3.44 -4.10                         kappa -0.44 -3.21 5.04  0.00

compute             mythermo all temp
thermo              100
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

fix         mvv     all mvv/edpd 0.5
fix         upper   all edpd/source cuboid 0.0  5.0 0.0 20.0 10.0 10.0  0.01
fix         lower   all edpd/source 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 edpd, 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) = 11.64 | 11.64 | 11.64 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            1    48.948932            0    50.448838    201.73366 
     100    1.0069712    43.754293            0    45.264656     199.5369 
     200   0.98667561    43.716052            0    45.195973    196.72854 
     300    1.0036944    43.706299            0    45.211746    195.35714 
     400    1.0024228    43.697014            0    45.200554     197.0062 
     500   0.99968161    43.687445            0    45.186873    193.80596 
Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms

Performance: 5346.567 tau/day, 6.188 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    | 75.106     | 75.106     | 75.106     |   0.0 | 92.95
Neigh   | 4.9836     | 4.9836     | 4.9836     |   0.0 |  6.17
Comm    | 0.31199    | 0.31199    | 0.31199    |   0.0 |  0.39
Output  | 0.00048232 | 0.00048232 | 0.00048232 |   0.0 |  0.00
Modify  | 0.29985    | 0.29985    | 0.29985    |   0.0 |  0.37
Other   |            | 0.09751    |            |       |  0.12

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:    749111 ave 749111 max 749111 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749111
Ave neighs/atom = 46.8194
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep      0

compute     temp    all edpd/temp/atom
compute     ccT     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

run                 500
Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0   0.99968161    43.687397            0    45.186825    196.38426 
     100    1.0041443    43.668196            0    45.174318    195.38066 
     200   0.99628392    43.666173            0    45.160505    197.84675 
     300    1.0029116     43.66224            0    45.166513    199.67414 
     400   0.99922193     43.64406            0    45.142799    196.94404 
     500   0.99355431    43.623266            0    45.113505    195.94136 
Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms

Performance: 5348.242 tau/day, 6.190 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    | 75.073     | 75.073     | 75.073     |   0.0 | 92.94
Neigh   | 4.8786     | 4.8786     | 4.8786     |   0.0 |  6.04
Comm    | 0.31086    | 0.31086    | 0.31086    |   0.0 |  0.38
Output  | 0.00045919 | 0.00045919 | 0.00045919 |   0.0 |  0.00
Modify  | 0.4139     | 0.4139     | 0.4139     |   0.0 |  0.51
Other   |            | 0.09731    |            |       |  0.12

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:    749667 ave 749667 max 749667 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749667
Ave neighs/atom = 46.8542
Neighbor list builds = 178
Dangerous builds = 0

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

Total wall time: 0:02:41
