forked from lijiext/lammps
165 lines
6.4 KiB
Groff
165 lines
6.4 KiB
Groff
LAMMPS (30 Apr 2015)
|
|
# 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)
|
|
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 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
|
|
master list distance cutoff = 4.8
|
|
Memory usage per processor = 4.16784 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 2.1708593 -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 0.510897 on 4 procs for 2000 steps with 400 atoms
|
|
|
|
Pair time (%) = 0.387877 (75.9208)
|
|
Neigh time (%) = 0.00349677 (0.684437)
|
|
Comm time (%) = 0.0481279 (9.42028)
|
|
Outpt time (%) = 0.000421941 (0.0825884)
|
|
Other time (%) = 0.070973 (13.8919)
|
|
|
|
Nlocal: 100 ave 108 max 95 min
|
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
|
Nghost: 125.75 ave 128 max 123 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Neighs: 482.25 ave 535 max 442 min
|
|
Histogram: 1 1 0 0 0 1 0 0 0 1
|
|
|
|
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 = 4.16867 Mbytes
|
|
Step 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 1.3461096 1654.9587
|
|
2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587
|
|
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
|
|
3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587
|
|
3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587
|
|
3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587
|
|
3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587
|
|
3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587
|
|
3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587
|
|
3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587
|
|
3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587
|
|
3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587
|
|
3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587
|
|
4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587
|
|
Loop time of 0.844572 on 4 procs for 2000 steps with 400 atoms
|
|
|
|
Pair time (%) = 0.713989 (84.5386)
|
|
Neigh time (%) = 0.00132543 (0.156935)
|
|
Comm time (%) = 0.0913201 (10.8126)
|
|
Outpt time (%) = 0.000489593 (0.0579693)
|
|
Other time (%) = 0.0374479 (4.43394)
|
|
|
|
Nlocal: 100 ave 103 max 96 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Nghost: 118 ave 122 max 115 min
|
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
|
Neighs: 464.25 ave 489 max 449 min
|
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
|
|
|
Total # of neighbors = 1857
|
|
Ave neighs/atom = 4.6425
|
|
Neighbor list builds = 48
|
|
Dangerous builds = 0
|