forked from lijiext/lammps
183 lines
7.4 KiB
Groff
183 lines
7.4 KiB
Groff
LAMMPS (15 Feb 2016)
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# RESquared ellipsoids in LJ background fluid
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units lj
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atom_style ellipsoid
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dimension 2
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lattice sq 0.02
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Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 400 atoms
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set group all type/fraction 2 0.1 95392
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45 settings made for type/fraction
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set type 1 mass 1.0
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355 settings made for mass
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set type 2 mass 1.5
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45 settings made for mass
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set type 1 shape 1 1 1
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355 settings made for shape
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set type 2 shape 3 1 1
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45 settings made for shape
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set group all quat/random 18238
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400 settings made for quat/random
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compute rot all temp/asphere
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group spheroid type 1
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355 atoms in group spheroid
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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compute_modify rot extra 357
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velocity all create 2.4 87287 loop geom
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pair_style resquared 4.0
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pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
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neighbor 0.8 bin
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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timestep 0.002
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compute q all property/atom quatw quati quatj quatk
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#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]
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#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
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#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
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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
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fix 2 all enforce2d
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compute_modify 1_temp extra ${dof}
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compute_modify 1_temp extra 357
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# equilibrate to shrink box around dilute system
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run 2000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.8
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ghost atom cutoff = 4.8
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binsize = 2.4 -> bins = 59 59 3
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Memory usage per processor = 4.17878 Mbytes
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Step rot E_pair TotEng Press Volume
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0 2.2718861 0 2.394 0.04788 20000
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100 1.7443002 0 1.8380563 0.03576216 20558.672
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200 2.2770454 0 2.3994366 0.046545139 20620.298
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300 1.8573283 0 1.9571597 0.04240689 18460.771
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400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
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500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
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600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
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700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
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800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
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900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
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1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
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1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
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1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
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1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
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1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
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1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
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1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
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1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
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1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
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1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
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2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
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Loop time of 1.79538 on 1 procs for 2000 steps with 400 atoms
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Performance: 192494.490 tau/day, 1113.973 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 1.582 | 1.582 | 1.582 | 0.0 | 88.12
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Neigh | 0.013545 | 0.013545 | 0.013545 | 0.0 | 0.75
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Comm | 0.0087712 | 0.0087712 | 0.0087712 | 0.0 | 0.49
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Output | 0.00034428 | 0.00034428 | 0.00034428 | 0.0 | 0.02
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Modify | 0.18736 | 0.18736 | 0.18736 | 0.0 | 10.44
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Other | | 0.003359 | | | 0.19
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Nlocal: 400 ave 400 max 400 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 216 ave 216 max 216 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1929 ave 1929 max 1929 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1929
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Ave neighs/atom = 4.8225
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Neighbor list builds = 177
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Dangerous builds = 146
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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Memory usage per processor = 4.18079 Mbytes
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Step rot E_pair TotEng Press Volume
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2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
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2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
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2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
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2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
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2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
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2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
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2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
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2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587
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2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587
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2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
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3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587
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3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587
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3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587
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3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587
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3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587
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3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587
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3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587
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3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587
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3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587
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3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587
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4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587
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Loop time of 3.05676 on 1 procs for 2000 steps with 400 atoms
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Performance: 113061.044 tau/day, 654.288 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 2.9201 | 2.9201 | 2.9201 | 0.0 | 95.53
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Neigh | 0.0051684 | 0.0051684 | 0.0051684 | 0.0 | 0.17
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Comm | 0.011668 | 0.011668 | 0.011668 | 0.0 | 0.38
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Output | 0.00038481 | 0.00038481 | 0.00038481 | 0.0 | 0.01
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Modify | 0.1134 | 0.1134 | 0.1134 | 0.0 | 3.71
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Other | | 0.00608 | | | 0.20
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Nlocal: 400 ave 400 max 400 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 204 ave 204 max 204 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1857 ave 1857 max 1857 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1857
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Ave neighs/atom = 4.6425
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Neighbor list builds = 48
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Dangerous builds = 0
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Total wall time: 0:00:04
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