forked from lijiext/lammps
190 lines
7.8 KiB
Groff
190 lines
7.8 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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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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Time spent = 0.00047946 secs
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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 ${dof}
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compute_modify rot extra/dof 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 ${dof}
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compute_modify 1_temp extra/dof 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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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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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair resquared, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 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 1.7443419 0 1.8381003 0.035765442 20557.278
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200 2.2768798 0 2.3992621 0.046544845 20618.928
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300 1.8573086 0 1.9571389 0.04239709 18464.842
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400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864
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500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958
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600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892
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700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262
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800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933
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900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139
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1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133
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1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229
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1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187
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1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057
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1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359
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1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976
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1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576
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1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102
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1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953
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1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914
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2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
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Loop time of 0.513811 on 4 procs for 2000 steps with 400 atoms
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Performance: 672620.799 tau/day, 3892.481 timesteps/s
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97.3% CPU use with 4 MPI tasks x 1 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 | 0.3553 | 0.36778 | 0.37737 | 1.4 | 71.58
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Neigh | 0.0039301 | 0.0040173 | 0.004127 | 0.1 | 0.78
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Comm | 0.056627 | 0.065564 | 0.076112 | 3.0 | 12.76
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Output | 0.00041318 | 0.00061768 | 0.0012202 | 0.0 | 0.12
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Modify | 0.070257 | 0.072503 | 0.074547 | 0.6 | 14.11
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Other | | 0.003331 | | | 0.65
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Nlocal: 100 ave 108 max 96 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 123.5 ave 125 max 122 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 471 ave 518 max 433 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Total # of neighbors = 1884
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Ave neighs/atom = 4.71
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Neighbor list builds = 177
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Dangerous builds = 144
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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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Per MPI rank memory allocation (min/avg/max) = 4.739 | 4.739 | 4.739 Mbytes
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Step c_rot E_pair TotEng Press Volume
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2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
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2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751
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2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751
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2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751
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2400 1.9752559 0.16967804 2.1177286 1.303768 1669.0751
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2500 1.978203 0.16642165 2.1631435 1.2908362 1669.0751
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2600 1.9587508 0.18695271 2.1506896 1.3513902 1669.0751
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2700 1.9654455 0.17997218 2.1247901 1.3360492 1669.0751
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2800 1.9870267 0.15716584 2.1207709 1.2045104 1669.0751
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2900 1.9230662 0.22448703 2.1353571 1.4964289 1669.0751
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3000 2.0042113 0.13903204 2.1149787 1.210065 1669.0751
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3100 1.9543694 0.19149467 2.0984705 1.3409714 1669.0751
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3200 1.9991114 0.14441984 2.1292354 1.1756471 1669.0751
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3300 1.9629781 0.18246618 2.1463676 1.3162687 1669.0751
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3400 1.940353 0.20630269 2.1687038 1.4952819 1669.0751
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3500 1.9887413 0.15531296 2.1485274 1.2530446 1669.0751
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3600 1.9732704 0.17171758 2.1755757 1.295861 1669.0751
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3700 2.0072863 0.13576402 2.1212392 1.1421254 1669.0751
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3800 1.9581337 0.18761851 2.1743384 1.3710796 1669.0751
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3900 1.9761519 0.16864273 2.142963 1.3037308 1669.0751
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4000 1.9615865 0.18390288 2.1244667 1.4179575 1669.0751
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Loop time of 0.846017 on 4 procs for 2000 steps with 400 atoms
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Performance: 408502.313 tau/day, 2364.018 timesteps/s
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97.4% CPU use with 4 MPI tasks x 1 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 | 0.63647 | 0.67097 | 0.74711 | 5.4 | 79.31
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Neigh | 0.0015061 | 0.0015807 | 0.0017054 | 0.2 | 0.19
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Comm | 0.058258 | 0.1341 | 0.16808 | 12.1 | 15.85
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Output | 0.00045156 | 0.00077933 | 0.0016997 | 0.0 | 0.09
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Modify | 0.028721 | 0.029793 | 0.03152 | 0.6 | 3.52
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Other | | 0.0088 | | | 1.04
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Nlocal: 100 ave 106 max 97 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 114 ave 117 max 111 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 468 ave 528 max 431 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Total # of neighbors = 1872
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Ave neighs/atom = 4.68
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Neighbor list builds = 50
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Dangerous builds = 0
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Total wall time: 0:00:01
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