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lammps/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1
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log.5Oct16.ellipse.resquared.g++.1
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LAMMPS (5 Oct 2016)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.17878 Mbytes
Step c_rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
Loop time of 1.69003 on 1 procs for 2000 steps with 400 atoms
Performance: 204492.823 tau/day, 1183.408 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 | 1.4827 | 1.4827 | 1.4827 | 0.0 | 87.73
Neigh | 0.014216 | 0.014216 | 0.014216 | 0.0 | 0.84
Comm | 0.0084538 | 0.0084538 | 0.0084538 | 0.0 | 0.50
Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02
Modify | 0.18062 | 0.18062 | 0.18062 | 0.0 | 10.69
Other | | 0.003745 | | | 0.22
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1929 ave 1929 max 1929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1929
Ave neighs/atom = 4.8225
Neighbor list builds = 177
Dangerous builds = 146
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18079 Mbytes
Step c_rot E_pair TotEng Press Volume
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587
2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587
3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587
3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587
3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587
3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587
3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587
3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587
3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587
3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587
3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587
4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587
Loop time of 2.86686 on 1 procs for 2000 steps with 400 atoms
Performance: 120550.133 tau/day, 697.628 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7349 | 2.7349 | 2.7349 | 0.0 | 95.40
Neigh | 0.0052247 | 0.0052247 | 0.0052247 | 0.0 | 0.18
Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.39
Output | 0.00036931 | 0.00036931 | 0.00036931 | 0.0 | 0.01
Modify | 0.10925 | 0.10925 | 0.10925 | 0.0 | 3.81
Other | | 0.005949 | | | 0.21
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 204 ave 204 max 204 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1857 ave 1857 max 1857 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1857
Ave neighs/atom = 4.6425
Neighbor list builds = 48
Dangerous builds = 0
Total wall time: 0:00:04
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