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lammps/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4
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LAMMPS (11 Aug 2017)
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### 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 ###
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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 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)
2 by 2 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) = 4.814 | 4.823 | 4.829 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 199.65978
50 1.0153476 43.948796 0 45.471722 198.3346
100 1.0064284 43.754875 0 45.264424 197.5308
150 0.99609985 43.726751 0 45.220807 197.50623
200 1.0016604 43.720283 0 45.22268 197.81129
250 1.0054979 43.718568 0 45.22672 195.79405
300 0.9997618 43.716617 0 45.216166 197.84788
350 0.99170101 43.72093 0 45.208389 196.07711
400 1.0043692 43.71648 0 45.22294 199.55247
450 1.0086263 43.709988 0 45.222833 198.20516
500 1.0029076 43.717879 0 45.222146 197.26281
Loop time of 24.5533 on 4 procs for 500 steps with 16000 atoms
Performance: 17594.412 tau/day, 20.364 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 | 22.236 | 22.418 | 22.736 | 4.0 | 91.30
Neigh | 1.2759 | 1.2883 | 1.3077 | 1.1 | 5.25
Comm | 0.35749 | 0.69526 | 0.88462 | 24.1 | 2.83
Output | 0.00043321 | 0.00050318 | 0.00070691 | 0.0 | 0.00
Modify | 0.11555 | 0.11648 | 0.11888 | 0.4 | 0.47
Other | | 0.03473 | | | 0.14
Nlocal: 4000 ave 4012 max 3982 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 5986.25 ave 6016 max 5956 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 187309 ave 188264 max 186087 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 749235
Ave neighs/atom = 46.8272
Neighbor list builds = 180
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) = 5.065 | 5.074 | 5.082 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0029076 43.717879 0 45.222146 198.45789
50 1.0077982 43.713264 0 45.224867 196.56183
100 1.0036823 43.708022 0 45.213451 196.00815
Loop time of 4.79577 on 4 procs for 100 steps with 16000 atoms
Performance: 18015.870 tau/day, 20.852 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 | 4.3481 | 4.39 | 4.4398 | 1.7 | 91.54
Neigh | 0.25477 | 0.25675 | 0.25963 | 0.4 | 5.35
Comm | 0.059327 | 0.11194 | 0.15608 | 11.0 | 2.33
Output | 0.00011206 | 0.00011748 | 0.00011992 | 0.0 | 0.00
Modify | 0.030417 | 0.030622 | 0.030739 | 0.1 | 0.64
Other | | 0.006301 | | | 0.13
Nlocal: 4000 ave 4010 max 3987 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 5985.25 ave 6025 max 5959 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 187304 ave 188092 max 186449 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 749216
Ave neighs/atom = 46.826
Neighbor list builds = 38
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29
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