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)
  2 by 2 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) = 4.969 | 4.979 | 4.985 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            1    48.948932            0    50.448838    199.51547 
     100    1.0106415    43.744371            0    45.260239    196.39598 
     200    1.0053215    43.714413            0    45.222301    195.35298 
     300   0.99886399    43.713356            0    45.211559    196.74821 
     400    1.0035264    43.699086            0    45.204282    195.47446 
     500    1.0025285    43.698051            0     45.20175    197.27042 
Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms

Performance: 20411.046 tau/day, 23.624 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 18.713     | 19.101     | 19.41      |   6.0 | 90.25
Neigh   | 1.2687     | 1.2925     | 1.3177     |   1.5 |  6.11
Comm    | 0.33013    | 0.66337    | 1.0747     |  34.3 |  3.13
Output  | 0.00023484 | 0.00028092 | 0.00036526 |   0.0 |  0.00
Modify  | 0.073931   | 0.075277   | 0.076306   |   0.3 |  0.36
Other   |            | 0.03227    |            |       |  0.15

Nlocal:    4000 ave 4067 max 3930 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:    5997.5 ave 6052 max 5943 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:    187388 ave 193157 max 181221 min
Histogram: 1 1 0 0 0 0 0 0 0 2

Total # of neighbors = 749552
Ave neighs/atom = 46.847
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) = 5.221 | 5.23 | 5.236 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1.0025285     43.69801            0    45.201708    194.00452 
     100    0.9885969    43.679927            0     45.16273    196.28442 
     200    1.0028463    43.663067            0    45.167242    198.25592 
     300    1.0027516    43.648817            0    45.152851    198.82226 
     400   0.99695312    43.641469            0    45.136805    197.97499 
     500   0.98202292    43.627163            0    45.100105    199.16319 
Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms

Performance: 20022.203 tau/day, 23.174 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 18.438     | 19.121     | 19.812     |  14.1 | 88.62
Neigh   | 1.2568     | 1.2885     | 1.325      |   2.5 |  5.97
Comm    | 0.29482    | 1.0219     | 1.7352     |  63.9 |  4.74
Output  | 0.00027728 | 0.00029719 | 0.0003531  |   0.0 |  0.00
Modify  | 0.11153    | 0.11265    | 0.1135     |   0.2 |  0.52
Other   |            | 0.03194    |            |       |  0.15

Nlocal:    4000 ave 4092 max 3899 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:    5974 ave 6019 max 5915 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs:    187414 ave 196149 max 178418 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 749658
Ave neighs/atom = 46.8536
Neighbor list builds = 181
Dangerous builds = 0

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

Total wall time: 0:00:42
