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lammps/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1
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log.15Feb16.ellipse.gayberne.g++.1
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LAMMPS (15 Feb 2016)
# GayBerne 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 gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 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.gayberne # 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 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 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
Loop time of 1.034 on 1 procs for 2000 steps with 400 atoms
Performance: 334235.078 tau/day, 1934.231 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 | 0.82535 | 0.82535 | 0.82535 | 0.0 | 79.82
Neigh | 0.01368 | 0.01368 | 0.01368 | 0.0 | 1.32
Comm | 0.011166 | 0.011166 | 0.011166 | 0.0 | 1.08
Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.03
Modify | 0.17955 | 0.17955 | 0.17955 | 0.0 | 17.36
Other | | 0.003941 | | | 0.38
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3031 ave 3031 max 3031 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3031
Ave neighs/atom = 7.5775
Neighbor list builds = 140
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18892 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026
2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026
2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026
2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026
2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026
2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026
2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026
2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026
3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026
3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026
3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026
3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026
3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026
3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026
3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026
3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026
3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026
3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026
4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026
Loop time of 1.15469 on 1 procs for 2000 steps with 400 atoms
Performance: 299301.907 tau/day, 1732.071 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 | 1.0251 | 1.0251 | 1.0251 | 0.0 | 88.77
Neigh | 0.0063124 | 0.0063124 | 0.0063124 | 0.0 | 0.55
Comm | 0.011792 | 0.011792 | 0.011792 | 0.0 | 1.02
Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.03
Modify | 0.10537 | 0.10537 | 0.10537 | 0.0 | 9.13
Other | | 0.005782 | | | 0.50
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 219 ave 219 max 219 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3046 ave 3046 max 3046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3046
Ave neighs/atom = 7.615
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02
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