Homec4science
Diffusion lammps (master) Browse

lammps/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1
f945d4567d4fmaster

Last Change
Raw File

log.16Aug17.edpd.g++.1
View Options

LAMMPS (11 Aug 2017)
########################################################################
### 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 ###
########################################################################
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
c4science · Help