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# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
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#dump 1 all atom 100 dump.obstacle
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 73 32 1
Memory usage per processor = 2.47903 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
3000 1 -0.52004759 0 0.16655839 1.417774 1324.489
4000 1 -0.5052153 0 0.18139068 1.4877209 1370.8743
5000 1 -0.49501138 0 0.1915946 1.2415582 1408.4993
6000 1 -0.45834057 0 0.22826542 1.2577643 1433.2191
7000 1 -0.44788351 0 0.23872247 1.1057853 1452.7011
8000 1 -0.42511924 0 0.26148674 1.1445522 1453.2588
9000 1 -0.35807547 0 0.32853051 1.0527564 1449.2608
10000 1 -0.38692228 0 0.2996837 1.0338935 1447.9561
11000 1 -0.38893457 0 0.29767141 1.0095645 1451.1231
12000 1 -0.35706485 0 0.32954114 1.0796623 1453.0879
13000 1 -0.39551125 0 0.29109474 1.0390286 1453.2992
14000 1 -0.38153043 0 0.30507555 0.98105926 1452.5639
15000 1 -0.38762689 0 0.29897909 1.1442417 1452.0174
16000 1 -0.3685331 0 0.31807289 1.0032132 1458.431
17000 1 -0.36299809 0 0.32360789 0.93727845 1460.2986
18000 1 -0.35752931 0 0.32907667 0.98337283 1458.583
19000 1 -0.38350344 0 0.30310254 1.0148373 1458.9749
20000 1 -0.35659703 0 0.33000895 1.0264431 1460.0031
21000 1 -0.36878002 0 0.31782596 1.0877739 1455.1053
22000 1 -0.37986917 0 0.30673681 1.129754 1455.0258
23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771
24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903
25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391
Loop time of 1.64517 on 1 procs for 25000 steps with 769 atoms
Performance: 3938793.608 tau/day, 15195.963 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 | 0.5054 | 0.5054 | 0.5054 | 0.0 | 30.72
Neigh | 0.17887 | 0.17887 | 0.17887 | 0.0 | 10.87
Comm | 0.022527 | 0.022527 | 0.022527 | 0.0 | 1.37
Output | 0.00023794 | 0.00023794 | 0.00023794 | 0.0 | 0.01
Modify | 0.85127 | 0.85127 | 0.85127 | 0.0 | 51.74
Other | | 0.08687 | | | 5.28
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1618 ave 1618 max 1618 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1618
Ave neighs/atom = 2.10403
Neighbor list builds = 1622
Dangerous builds = 0
Total wall time: 0:00:01