146 lines
8.8 KiB
Groff
146 lines
8.8 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### overdamped dynamics of non-interacting ellipsoids in 3D #####
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variable rng string uniform
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variable seed string 198098
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variable temp string 1.0
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variable gamma_r_1 string 2.0
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variable gamma_r_2 string 0.25
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variable gamma_r_3 string 0.1
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variable gamma_t_1 string 5.0
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variable gamma_t_2 string 7.0
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variable gamma_t_3 string 9.0
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variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
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variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
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variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
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units lj
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atom_style hybrid dipole ellipsoid
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WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
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dimension 3
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newton off
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lattice sc 0.4
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Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
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region box block -8 8 -8 8 -8 8
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create_box 1 box
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Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
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2 by 1 by 2 MPI processor grid
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create_atoms 1 box
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Created 4096 atoms
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create_atoms CPU = 0.002 seconds
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mass * 1.0
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set type * dipole/random ${seed} 1.0
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set type * dipole/random 198098 1.0
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Setting atom values ...
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4096 settings made for dipole/random
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set type * shape 3.0 1.0 1.0
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Setting atom values ...
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4096 settings made for shape
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set type * quat/random ${seed}
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set type * quat/random 198098
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Setting atom values ...
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4096 settings made for quat/random
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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pair_style none
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fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 100
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# main run
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run 3000
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WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
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Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
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0 1.4996338 0 0 0 0 0
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100 45236.508 0 0.00030817418 0.00030717742 0.0003019227 0.0009172743
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200 45564.566 0 0.00062027526 0.00062110132 0.0006080391 0.0018494157
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300 46232.801 0 0.00091155216 0.00094473459 0.00093009391 0.0027863807
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400 45250.414 0 0.0011980791 0.0012538262 0.0012201461 0.0036720513
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500 45217.133 0 0.0015186813 0.0015752994 0.001509437 0.0046034177
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600 45531.276 0 0.0018194588 0.0019243758 0.0018209246 0.0055647592
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700 44834.624 0 0.0021277747 0.0022417115 0.0021352036 0.0065046898
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800 45413.998 0 0.0024558838 0.0025741787 0.0024088704 0.0074389329
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900 45668.624 0 0.0027366171 0.002858242 0.0027580782 0.0083529374
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1000 45809.223 0 0.0030331425 0.003186293 0.0030414906 0.0092609261
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1100 45193.019 0 0.0033199824 0.0034668659 0.003298885 0.010085733
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1200 44522.927 0 0.0036503132 0.0037490684 0.0036089852 0.011008367
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1300 45214.567 0 0.0039958617 0.0040881934 0.0038709079 0.011954963
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1400 45217.997 0 0.004276499 0.0044624985 0.0041104891 0.012849487
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1500 45497.171 0 0.0045943272 0.0047116875 0.0044113504 0.013717365
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1600 45905.187 0 0.0049004996 0.0049982014 0.0047394999 0.014638201
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1700 45551.346 0 0.0051540939 0.0053187249 0.0050861052 0.015558924
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1800 45347.782 0 0.0054101891 0.0056306 0.0053515873 0.016392376
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1900 45107.895 0 0.005743705 0.0059584896 0.0056220384 0.017324233
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2000 45043.389 0 0.0059803588 0.006230449 0.005911555 0.018122363
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2100 45433.293 0 0.0062610364 0.0066140744 0.0062152977 0.019090408
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2200 45804.217 0 0.0064995183 0.0068831274 0.0064971789 0.019879825
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2300 45697.516 0 0.0067910846 0.0071845673 0.0068046192 0.020780271
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2400 45447.422 0 0.0071022706 0.0074743709 0.0070983185 0.02167496
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2500 45395.18 0 0.0073817023 0.0077467991 0.0074263196 0.022554821
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2600 45943.044 0 0.0075953233 0.007997707 0.0076508583 0.023243889
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2700 45859.978 0 0.0079082128 0.0082090043 0.0078853376 0.024002555
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2800 45822.007 0 0.0082607534 0.0084510061 0.0081985549 0.024910314
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2900 45438.456 0 0.0085958203 0.0088807705 0.0084755353 0.025952126
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3000 45060.957 0 0.0089017992 0.0090966159 0.0086718875 0.026670303
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Loop time of 1.23282 on 4 procs for 3000 steps with 4096 atoms
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Performance: 2102.502 tau/day, 2433.452 timesteps/s
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97.9% 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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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.00
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Comm | 0.10931 | 0.11473 | 0.11748 | 0.9 | 9.31
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Output | 0.001375 | 0.0018924 | 0.0034099 | 2.0 | 0.15
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Modify | 0.97744 | 0.99158 | 1.0089 | 1.3 | 80.43
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Other | | 0.1246 | | | 10.11
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Nlocal: 1024.00 ave 1035 max 1016 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0.0000000
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:01
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