127 lines
6.4 KiB
Groff
127 lines
6.4 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 a sphere (with dipole attached to it) 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_t string 5.0
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variable gamma_r string 0.7
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variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
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variable params string uniform_${temp}_${gamma_r}_${gamma_t}
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variable params string uniform_1.0_${gamma_r}_${gamma_t}
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variable params string uniform_1.0_0.7_${gamma_t}
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variable params string uniform_1.0_0.7_5.0
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units lj
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atom_style hybrid dipole sphere
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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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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/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
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fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
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fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
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fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
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fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
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fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${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) = 4.737 | 4.737 | 4.737 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 32032.279 0 0.00040227568 0.00039159837 0.00040147813 0.0011953522
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200 31673.093 0 0.00077657885 0.00077292327 0.00079963705 0.0023491392
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300 31476.164 0 0.0011712083 0.0011606723 0.0012089537 0.0035408343
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400 31911.374 0 0.0015803424 0.001562091 0.0016042321 0.0047466655
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500 31182.011 0 0.0019677217 0.0019269105 0.0020015977 0.0058962298
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600 31206.05 0 0.0023360975 0.0023134398 0.0024213372 0.0070708745
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700 31278.057 0 0.0026966955 0.0027129858 0.0028721373 0.0082818187
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800 31677.724 0 0.0031197964 0.003134834 0.0032726303 0.0095272607
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900 31312.741 0 0.0035636612 0.0035573653 0.0037328373 0.010853864
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1000 31426.075 0 0.0039774626 0.003952159 0.0041879386 0.01211756
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1100 31361.699 0 0.0044256852 0.004320566 0.004638132 0.013384383
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1200 31559.778 0 0.0048338539 0.0047210601 0.0050296056 0.01458452
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1300 31716.797 0 0.0052239651 0.0050796723 0.0054794684 0.015783106
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1400 31231.077 0 0.0055890568 0.005472377 0.0059264123 0.016987846
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1500 31605.513 0 0.0059876582 0.0058974054 0.0063452478 0.018230311
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1600 31551.402 0 0.006413094 0.0062665632 0.0067442106 0.019423868
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1700 31725.868 0 0.0068244611 0.0067189707 0.0071424779 0.02068591
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1800 31385.794 0 0.0071570297 0.0070502303 0.0075240296 0.02173129
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1900 31754.094 0 0.0075638662 0.0074243015 0.0079935325 0.0229817
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2000 31668.959 0 0.0080059944 0.0079019753 0.0084000614 0.024308031
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2100 31781.994 0 0.0084108141 0.0082719077 0.0088004977 0.02548322
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2200 31455.021 0 0.0088844434 0.0086931769 0.0091916929 0.026769313
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2300 31273.079 0 0.0093155639 0.0091027782 0.0095364621 0.027954804
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2400 31283.781 0 0.0098441686 0.0094496218 0.0099279073 0.029221698
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2500 31758.315 0 0.010372129 0.0097843406 0.010334653 0.030491123
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2600 31780.442 0 0.010770862 0.010313119 0.010637545 0.031721525
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2700 31552.277 0 0.011268703 0.010693437 0.01110762 0.033069759
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2800 31124.693 0 0.011661333 0.011100115 0.011480624 0.034242072
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2900 31438.795 0 0.012068847 0.011346633 0.011842006 0.035257486
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3000 31574.258 0 0.012482632 0.011691477 0.012210207 0.036384317
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Loop time of 2.8531 on 1 procs for 3000 steps with 4096 atoms
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Performance: 908.486 tau/day, 1051.488 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 | 3.2425e-05 | 3.2425e-05 | 3.2425e-05 | 0.0 | 0.00
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Comm | 0.13219 | 0.13219 | 0.13219 | 0.0 | 4.63
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Output | 0.0045686 | 0.0045686 | 0.0045686 | 0.0 | 0.16
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Modify | 2.5857 | 2.5857 | 2.5857 | 0.0 | 90.63
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Other | | 0.1307 | | | 4.58
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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: 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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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 = 1
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Dangerous builds = 0
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Total wall time: 0:00:02
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