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log.lammps
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LAMMPS (29 Oct 2020)
info all out overwrite tmp.txt
# 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 = 1.2843567 2.2245711 1.2843567
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0.0000000 0.0000000 -0.32108918) to (51.374269 22.245711 0.32108918)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
create_atoms CPU = 0.001 seconds
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
Setting atom values ...
120 settings made for type
set group upper type 3
Setting atom values ...
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
region 3 sphere 32.58535855914569 4.405990175849329 0 3
region 4 sphere 23.445967154523856 5.470297874475864 0 3
delete_atoms region 3
Deleted 34 atoms, new total = 806
fix 7 flow indent 100 sphere 32.58535855914569 4.405990175849329 0 4
delete_atoms region 4
Deleted 34 atoms, new total = 772
fix 8 flow indent 100 sphere 23.445967154523856 5.470297874475864 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:472)
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 ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.085 | 4.085 | 4.085 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0045485 0 0 0.69095238 0.466645 1143.0857
1000 1 -0.33073878 0 0.35708506 1.3381316 1274.0712
2000 1 -0.40363396 0 0.28418988 1.292515 1298.5599
3000 1 -0.51261439 0 0.17520944 1.7510276 1287.8328
4000 1 -0.49906101 0 0.18876282 1.6431521 1293.695
5000 1 -0.47646416 0 0.21135968 1.5346433 1313.9824
6000 1 -0.47515214 0 0.21267169 1.4784276 1319.5983
7000 1 -0.52038119 0 0.16744265 1.4300782 1317.6028
8000 1 -0.46227934 0 0.2255445 1.4825832 1328.3512
9000 1 -0.46187681 0 0.22594703 1.3442406 1332.2276
10000 1 -0.43475933 0 0.2530645 1.2675675 1337.4211
11000 1 -0.46667411 0 0.22114973 1.1971712 1340.9891
12000 1 -0.46185228 0 0.22597155 1.3008212 1340.7064
13000 1 -0.44189468 0 0.24592916 1.2564192 1342.7189
14000 1 -0.42468723 0 0.2631366 1.31056 1341.599
15000 1 -0.40845661 0 0.27936722 1.3403691 1343.6412
16000 1 -0.44547817 0 0.24234566 1.26814 1341.079
17000 1 -0.44385339 0 0.24397044 1.3358329 1338.3615
18000 1 -0.43498984 0 0.25283399 1.2720457 1338.7047
19000 1 -0.45746133 0 0.23036251 1.2251072 1336.9693
20000 1 -0.43683555 0 0.25098829 1.1933353 1333.7786
21000 1 -0.4707823 0 0.21704153 1.396608 1330.3514
22000 1 -0.43429532 0 0.25352851 1.2192229 1338.1346
23000 1 -0.445084 0 0.24273983 1.230664 1333.4048
24000 1 -0.45048501 0 0.23733882 1.2727724 1330.0038
25000 1 -0.44775858 0 0.24006526 1.2612923 1333.8176
Loop time of 4.57356 on 1 procs for 25000 steps with 772 atoms
Performance: 1416839.694 tau/day, 5466.203 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4336 | 1.4336 | 1.4336 | 0.0 | 31.34
Neigh | 0.32443 | 0.32443 | 0.32443 | 0.0 | 7.09
Comm | 0.05958 | 0.05958 | 0.05958 | 0.0 | 1.30
Output | 0.22305 | 0.22305 | 0.22305 | 0.0 | 4.88
Modify | 2.2918 | 2.2918 | 2.2918 | 0.0 | 50.11
Other | | 0.2411 | | | 5.27
Nlocal: 772.000 ave 772 max 772 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38.0000 ave 38 max 38 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1757.00 ave 1757 max 1757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1757
Ave neighs/atom = 2.2759067
Neighbor list builds = 1669
Dangerous builds = 0
Total wall time: 0:00:04