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lammps/examples/ellipse/log.ellipse.gayberne.18Feb13.linux.4
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LAMMPS (18 Feb 2013)
# 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)
2 by 2 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 1 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 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 = 3.8645 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 0.9525477 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
Loop time of 0.266395 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.128512 (48.2411)
Neigh time (%) = 0.00328618 (1.23358)
Comm time (%) = 0.043604 (16.3682)
Outpt time (%) = 0.0182753 (6.86024)
Other time (%) = 0.0727174 (27.2969)
Nlocal: 100 ave 113 max 79 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 139.75 ave 151 max 132 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 717 ave 880 max 487 min
Histogram: 1 0 0 0 0 1 0 1 0 1
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 = 3.8665 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981993 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222388 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099822 1187.4615
2500 2.0866909 -3.2692048 -1.1766063 0.67971376 1187.4615
2600 2.098286 -3.2774469 -1.1869922 0.90453433 1187.4615
2700 2.0482737 -3.2229412 -1.1928882 0.69426669 1187.4615
2800 1.9676254 -3.1400305 -1.1685788 0.75785389 1187.4615
2900 2.0421207 -3.2182098 -1.1866861 0.79382733 1187.4615
3000 2.1074356 -3.2870234 -1.2012809 0.18867661 1187.4615
3100 2.0466079 -3.2226774 -1.1821925 0.7048821 1187.4615
3200 2.1158976 -3.2976855 -1.1589624 0.5209376 1187.4615
3300 2.1508115 -3.3368934 -1.1793489 0.45871464 1187.4615
3400 2.1046063 -3.2881336 -1.1615171 0.71895972 1187.4615
3500 2.066052 -3.2475413 -1.1359344 0.77760912 1187.4615
3600 2.0042504 -3.1791312 -1.1647191 0.50555439 1187.4615
3700 1.9888544 -3.1596354 -1.1679759 0.4059197 1187.4615
3800 1.9919683 -3.1636959 -1.1860197 0.70259722 1187.4615
3900 2.056542 -3.2325648 -1.1700712 0.43059703 1187.4615
4000 1.9958145 -3.1666798 -1.2556316 0.87469089 1187.4615
Loop time of 0.286178 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.157163 (54.9177)
Neigh time (%) = 0.00151408 (0.529068)
Comm time (%) = 0.0698599 (24.4113)
Outpt time (%) = 0.0182382 (6.37301)
Other time (%) = 0.0394036 (13.7689)
Nlocal: 100 ave 118 max 69 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 139 ave 156 max 130 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 729.75 ave 951 max 409 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 2919
Ave neighs/atom = 7.2975
Neighbor list builds = 47
Dangerous builds = 0
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