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lammps/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1
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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)
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
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