186 lines
7.5 KiB
Groff
186 lines
7.5 KiB
Groff
LAMMPS (15 Feb 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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2 by 2 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 = 4.16784 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 2.1709732 -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 0.88473343 1121.7026
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Loop time of 0.513848 on 4 procs for 2000 steps with 400 atoms
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Performance: 672572.269 tau/day, 3892.201 timesteps/s
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88.1% CPU use with 4 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 | 0.19352 | 0.21426 | 0.23184 | 3.0 | 41.70
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Neigh | 0.0034561 | 0.0036583 | 0.0038161 | 0.3 | 0.71
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Comm | 0.10711 | 0.12693 | 0.14494 | 4.6 | 24.70
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Output | 0.0016916 | 0.0017142 | 0.0017467 | 0.1 | 0.33
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Modify | 0.14238 | 0.15759 | 0.16878 | 2.4 | 30.67
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Other | | 0.009694 | | | 1.89
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Nlocal: 100 ave 113 max 85 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Nghost: 149.75 ave 160 max 141 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 757.75 ave 885 max 592 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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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 = 4.16867 Mbytes
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Step rot E_pair TotEng Press Volume
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2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
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2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026
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2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
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2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026
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2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026
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2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026
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2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026
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2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026
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2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026
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2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026
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3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026
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3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026
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3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026
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3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026
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3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026
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3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026
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3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026
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3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026
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3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026
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3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026
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4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026
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Loop time of 0.373834 on 4 procs for 2000 steps with 400 atoms
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Performance: 924475.349 tau/day, 5349.973 timesteps/s
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99.7% CPU use with 4 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 | 0.25404 | 0.26703 | 0.29737 | 3.4 | 71.43
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Neigh | 0.0014787 | 0.0016722 | 0.0018535 | 0.3 | 0.45
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Comm | 0.036186 | 0.068545 | 0.082895 | 7.2 | 18.34
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Output | 0.00050688 | 0.00052452 | 0.00055194 | 0.1 | 0.14
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Modify | 0.025374 | 0.027727 | 0.030269 | 1.1 | 7.42
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Other | | 0.008336 | | | 2.23
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Nlocal: 100 ave 106 max 92 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Nghost: 148 ave 152 max 145 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 760.25 ave 815 max 713 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Total # of neighbors = 3041
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Ave neighs/atom = 7.6025
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Neighbor list builds = 46
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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: 0:00:00
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