Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1
4dae1d2d3b5defficient_neuronet

Last Change
Raw File

log.ellipse.gayberne.1Feb14.linux.1
View Options

LAMMPS (1 Feb 2014)
# 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
Memory usage per processor = 3.4108 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 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
Loop time of 0.725952 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.503768 (69.3941)
Neigh time (%) = 0.0126507 (1.74264)
Comm time (%) = 0.0136161 (1.87562)
Outpt time (%) = 0.000351191 (0.0483765)
Other time (%) = 0.195566 (26.9393)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 232 ave 232 max 232 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2868 ave 2868 max 2868 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.42095 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981994 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222377 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099841 1187.4615
2500 2.0866909 -3.2692047 -1.1766063 0.67971438 1187.4615
2600 2.0982853 -3.2774461 -1.1869918 0.9045362 1187.4615
2700 2.0482743 -3.2229418 -1.1928883 0.69426343 1187.4615
2800 1.9676269 -3.1400321 -1.1685787 0.7578428 1187.4615
2900 2.0421127 -3.2182014 -1.1866875 0.79386471 1187.4615
3000 2.1074286 -3.2870176 -1.2012732 0.18871121 1187.4615
3100 2.0466481 -3.2227223 -1.1821678 0.70482646 1187.4615
3200 2.1159694 -3.2976371 -1.1588561 0.52105755 1187.4615
3300 2.150544 -3.3366154 -1.179448 0.45837229 1187.4615
3400 2.1035378 -3.2868896 -1.1614884 0.72339226 1187.4615
3500 2.0665964 -3.2481259 -1.1351878 0.77887358 1187.4615
3600 2.0079794 -3.183204 -1.1647668 0.49419048 1187.4615
3700 2.0028597 -3.1740178 -1.1738107 0.38011763 1187.4615
3800 1.9501131 -3.1191211 -1.1785414 0.77609881 1187.4615
3900 2.0648034 -3.2412864 -1.1750708 0.55412858 1187.4615
4000 2.0161932 -3.1865719 -1.1939133 0.6656145 1187.4615
Loop time of 0.763192 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.621734 (81.4649)
Neigh time (%) = 0.0058322 (0.764184)
Comm time (%) = 0.0142851 (1.87175)
Outpt time (%) = 0.000369549 (0.0484215)
Other time (%) = 0.120971 (15.8507)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 220 ave 220 max 220 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2901 ave 2901 max 2901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2901
Ave neighs/atom = 7.2525
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help