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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1 by 1 by 1 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 = 0.005 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) = 5.219 | 5.219 | 5.219 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 45690.838 0 0.00029994317 0.00029953902 0.00030002809 0.00089951027
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200 45571.166 0 0.00061376797 0.00060955238 0.00061153551 0.0018348559
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300 44693.418 0 0.00093058034 0.00089383536 0.00091554588 0.0027399616
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400 44831.846 0 0.001250227 0.0012230128 0.0012120517 0.0036852914
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500 45028.015 0 0.0015448869 0.0015339549 0.0014978843 0.0045767262
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600 45895.442 0 0.0018621952 0.0018169905 0.0018352784 0.0055144641
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700 45858.744 0 0.0021617097 0.0021137714 0.0021360394 0.0064115206
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800 45155.215 0 0.002428445 0.0024288837 0.0024516737 0.0073090023
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900 45427.427 0 0.0027265978 0.0027662531 0.0027329878 0.0082258387
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1000 45398.166 0 0.0030685345 0.0030805014 0.0029765916 0.0091256275
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1100 44622.428 0 0.0033766954 0.0033976168 0.0032745406 0.010048853
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1200 45500.277 0 0.0036410565 0.0036840528 0.0035831659 0.010908275
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1300 45265.8 0 0.0039143146 0.0039419334 0.0038761633 0.011732411
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1400 45482.435 0 0.0042006542 0.0043373651 0.004164002 0.012702021
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1500 45126.629 0 0.0044647379 0.0046021855 0.004487041 0.013553965
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1600 45178.172 0 0.0047726618 0.0049110287 0.0048012671 0.014484958
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1700 44918.685 0 0.005104787 0.0052522662 0.0050844375 0.015441491
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1800 44776.678 0 0.0054395368 0.0056092038 0.0054623875 0.016511128
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1900 46035.987 0 0.0057735872 0.0059357043 0.0057296009 0.017438892
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2000 45436.517 0 0.0060837459 0.0063485717 0.0059769119 0.018409229
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2100 45871.502 0 0.0063736337 0.0066551978 0.0063077439 0.019336575
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2200 45511.847 0 0.0066419141 0.0069700452 0.0065553318 0.020167291
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2300 45597.047 0 0.0069251517 0.0073015716 0.0068945654 0.021121289
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2400 44832.007 0 0.0071894253 0.0076238221 0.0071638554 0.021977103
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2500 45668.42 0 0.0074351304 0.0079594991 0.0075390719 0.022933701
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2600 45248.483 0 0.007781496 0.008293944 0.0077956068 0.023871047
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2700 45308.515 0 0.0080302993 0.0086329679 0.0081457335 0.024809001
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2800 45637.72 0 0.0083889026 0.0089173198 0.0086032427 0.025909465
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2900 45909.343 0 0.0087169392 0.009181179 0.0088778569 0.026775975
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3000 45213.613 0 0.0090508891 0.0094253485 0.0092660321 0.02774227
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Loop time of 4.13937 on 1 procs for 3000 steps with 4096 atoms
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Performance: 626.183 tau/day, 724.749 timesteps/s
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99.9% CPU use with 1 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 | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.24709 | 0.24709 | 0.24709 | 0.0 | 5.97
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Output | 0.004636 | 0.004636 | 0.004636 | 0.0 | 0.11
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Modify | 3.7604 | 3.7604 | 3.7604 | 0.0 | 90.85
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Other | | 0.1272 | | | 3.07
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Nlocal: 4096.00 ave 4096 max 4096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 817.000 ave 817 max 817 min
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Histogram: 1 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: 1 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 = 0
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Dangerous builds = 0
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Total wall time: 0:00:04
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