forked from lijiext/lammps
186 lines
7.5 KiB
Groff
186 lines
7.5 KiB
Groff
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LAMMPS (5 Oct 2016)
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# GayBerne 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 gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1.0 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.gayberne # 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 c_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 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
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500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
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600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
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700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
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800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
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900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
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1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
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1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
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1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
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1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
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1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
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1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
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1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
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1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
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1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
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1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
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2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
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Loop time of 1.01022 on 1 procs for 2000 steps with 400 atoms
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Performance: 342102.068 tau/day, 1979.757 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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---------------------------------------------------------------
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Pair | 0.80465 | 0.80465 | 0.80465 | 0.0 | 79.65
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Neigh | 0.014326 | 0.014326 | 0.014326 | 0.0 | 1.42
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Comm | 0.011179 | 0.011179 | 0.011179 | 0.0 | 1.11
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Output | 0.00032926 | 0.00032926 | 0.00032926 | 0.0 | 0.03
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Modify | 0.17561 | 0.17561 | 0.17561 | 0.0 | 17.38
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Other | | 0.004126 | | | 0.41
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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: 249 ave 249 max 249 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3031 ave 3031 max 3031 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3031
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Ave neighs/atom = 7.5775
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Neighbor list builds = 140
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Dangerous builds = 80
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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 = 4.18892 Mbytes
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Step c_rot E_pair TotEng Press Volume
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2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
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2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026
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2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
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2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026
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2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026
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2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026
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2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026
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2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026
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2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026
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2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026
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3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026
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3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026
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3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026
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3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026
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3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026
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3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026
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3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026
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3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026
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3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026
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3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026
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4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026
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Loop time of 1.13656 on 1 procs for 2000 steps with 400 atoms
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Performance: 304074.636 tau/day, 1759.691 timesteps/s
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99.9% 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 | 1.0076 | 1.0076 | 1.0076 | 0.0 | 88.65
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Neigh | 0.0065663 | 0.0065663 | 0.0065663 | 0.0 | 0.58
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Comm | 0.011639 | 0.011639 | 0.011639 | 0.0 | 1.02
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Output | 0.00035858 | 0.00035858 | 0.00035858 | 0.0 | 0.03
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Modify | 0.10463 | 0.10463 | 0.10463 | 0.0 | 9.21
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Other | | 0.00581 | | | 0.51
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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: 219 ave 219 max 219 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3046 ave 3046 max 3046 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3046
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Ave neighs/atom = 7.615
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Neighbor list builds = 47
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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