Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/ellipse/log.ellipse.resquared.15Jan10.linux.1
9921249796c1efficient_neuronet

Last Change
Raw File

log.ellipse.resquared.15Jan10.linux.1
View Options

LAMMPS (15 Jan 2010)
# 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 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 group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
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
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
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared id type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
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
Memory usage per processor = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7442957 0 1.8380516 0.035762064 20558.675
200 2.2770743 0 2.399467 0.046545738 20620.294
300 1.8572884 0 1.9571177 0.042405959 18460.78
400 2.1709476 -2.7650868e-05 2.2876084 0.066840176 13689.499
500 1.9974207 0.016918546 2.0563673 0.11517079 8482.9842
600 2.0623605 0.078682156 2.0822655 0.2882877 4776.2504
700 2.110577 0.19687352 2.3261907 0.85200625 2756.4677
800 1.7458278 0.29268299 1.9788694 1.629108 1832.8121
900 1.7925286 0.2406461 2.0272778 1.7295734 1516.7707
1000 1.8280565 0.16642416 1.9844287 1.431503 1517.365
1100 2.1579097 0.10561885 2.2607523 0.98798133 1744.9685
1200 1.7966192 0.057740166 1.8308675 0.54361557 2182.8329
1300 2.2982919 0.036420252 2.3349773 0.45727558 2731.1191
1400 1.766633 0.038034214 1.7891558 0.32935291 3230.8068
1500 2.3052769 0.08089522 2.3763972 0.45778471 3432.038
1600 1.8587716 0.067481187 1.9188742 0.39446029 3276.3409
1700 2.1802595 0.13974472 2.3397684 0.70931895 2829.789
1800 1.9313351 0.14233089 2.0646735 0.83838184 2321.0971
1900 2.0664832 0.16461014 2.1858936 1.1676882 1900.719
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
Loop time of 2.31973 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 2.00801 (86.5624)
Neigh time (%) = 0.0140963 (0.607669)
Comm time (%) = 0.0165806 (0.714764)
Outpt time (%) = 0.0357938 (1.54302)
Other time (%) = 0.245245 (10.5721)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 207 ave 207 max 207 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1894 ave 1894 max 1894 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1894
Ave neighs/atom = 4.735
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5919 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
2100 1.9499859 0.15215993 2.1113673 1.1823056 1658.4096
2200 1.947135 0.15513968 2.1194838 1.2327003 1658.4096
2300 1.9248051 0.17868446 2.099053 1.3075669 1658.4096
2400 1.9130129 0.1909732 2.1178764 1.360918 1658.4096
2500 1.923006 0.18047305 2.0814946 1.300819 1658.4096
2600 1.9861146 0.11411525 2.0953259 1.0398086 1658.4096
2700 1.9100096 0.1941301 2.0711987 1.3442038 1658.4096
2800 1.9229156 0.18068074 2.0604436 1.3326935 1658.4096
2900 1.9390667 0.16374523 2.0849791 1.2648629 1658.4096
3000 1.8823323 0.22349204 2.0853271 1.5182106 1658.4096
3100 1.904216 0.20028068 2.0777595 1.3868716 1658.4096
3200 1.9189112 0.18492982 2.0694131 1.3303671 1658.4096
3300 1.8823023 0.22351465 2.0549802 1.569699 1658.4096
3400 1.9062111 0.19834548 2.0909028 1.452764 1658.4096
3500 1.9502999 0.15174971 2.0880306 1.2382643 1658.4096
3600 1.9785898 0.12200286 2.1051594 1.0976011 1658.4096
3700 1.8929662 0.21215612 2.0740516 1.4270687 1658.4096
3800 1.9312581 0.17171893 2.0694635 1.3048501 1658.4096
3900 1.9552568 0.14655904 2.09034 1.2083214 1658.4096
4000 1.9147099 0.18934973 2.104485 1.3672573 1658.4096
Loop time of 4.08906 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.81754 (93.3598)
Neigh time (%) = 0.00639486 (0.15639)
Comm time (%) = 0.0218513 (0.534384)
Outpt time (%) = 0.0360107 (0.880661)
Other time (%) = 0.207263 (5.06872)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 205 ave 205 max 205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1885 ave 1885 max 1885 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1885
Ave neighs/atom = 4.7125
Neighbor list builds = 46
Dangerous builds = 0
c4science · Help