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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)
4 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 = 2.47142 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
3000 1 -0.49062369 0 0.19598229 1.5239334 1322.2627
4000 1 -0.50088987 0 0.18571611 1.4614192 1367.6511
5000 1 -0.47747975 0 0.20912623 1.3417367 1405.501
6000 1 -0.47477948 0 0.21182651 1.3061542 1432.0778
7000 1 -0.44736042 0 0.23924556 1.1332701 1441.4911
8000 1 -0.42748547 0 0.25912051 1.0531138 1443.7226
9000 1 -0.41433123 0 0.27227475 1.0997172 1450.1414
10000 1 -0.38722477 0 0.29938121 1.0652717 1456.2877
11000 1 -0.40216239 0 0.28444359 1.1152975 1459.2764
12000 1 -0.38520467 0 0.30140132 0.94109687 1463.6094
13000 1 -0.38233942 0 0.30426656 1.0184283 1461.2151
14000 1 -0.38106329 0 0.3055427 0.93372261 1459.276
15000 1 -0.36896962 0 0.31763636 1.0015053 1456.4295
16000 1 -0.38669413 0 0.29991185 0.99320514 1460.5925
17000 1 -0.3879857 0 0.29862028 0.95908906 1461.1978
18000 1 -0.37448688 0 0.3121191 0.96871256 1460.7159
19000 1 -0.39700052 0 0.28960547 1.0770396 1458.2596
20000 1 -0.36125976 0 0.32534622 0.86282353 1466.9129
21000 1 -0.38882675 0 0.29777923 0.9877477 1457.4909
22000 1 -0.38158333 0 0.30502266 1.0184682 1454.5247
23000 1 -0.37327871 0 0.31332728 1.0623185 1453.1342
24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461
25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191
Loop time of 0.821326 on 4 procs for 25000 steps with 769 atoms
Performance: 7889678.376 tau/day, 30438.574 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.064561 | 0.12703 | 0.20657 | 15.5 | 15.47
Neigh | 0.036315 | 0.04798 | 0.06249 | 4.4 | 5.84
Comm | 0.14793 | 0.21791 | 0.27951 | 10.6 | 26.53
Output | 0.00043583 | 0.00046438 | 0.00054574 | 0.2 | 0.06
Modify | 0.27754 | 0.31239 | 0.3371 | 3.9 | 38.03
Other | | 0.1156 | | | 14.07
Nlocal: 192.25 ave 243 max 151 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 41.75 ave 43 max 39 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 408.5 ave 575 max 266 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 1634
Ave neighs/atom = 2.12484
Neighbor list builds = 1631
Dangerous builds = 1
Total wall time: 0:00:00