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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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 = 0.006 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) = 4.694 | 4.694 | 4.694 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 30882.707 0 0.00040787161 0.00039391576 0.00040796913 0.0012097565
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200 31370.751 0 0.00081742036 0.00078240455 0.0008195167 0.0024193416
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300 31469.51 0 0.0012118299 0.0011819412 0.0012477119 0.003641483
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400 31696.58 0 0.0015540547 0.0015849689 0.0015836091 0.0047226327
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500 31488.269 0 0.0019638041 0.0019659637 0.0020547832 0.005984551
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600 30942.589 0 0.0023273784 0.0023572171 0.0024715245 0.00715612
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700 31228.473 0 0.0027821732 0.002735338 0.0028734675 0.0083909787
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800 31426.92 0 0.0031663838 0.0031092782 0.0033231014 0.0095987634
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900 31447.595 0 0.003539588 0.003564381 0.003753036 0.010857005
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1000 31363.911 0 0.0039854308 0.003937555 0.0041203919 0.012043378
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1100 31522.958 0 0.0043009285 0.0043676491 0.0044799414 0.013148519
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1200 31403.033 0 0.0046361199 0.0047513598 0.0049014974 0.014288977
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1300 31752.182 0 0.0049824718 0.0051327113 0.0053130614 0.015428244
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1400 31336.955 0 0.0054251445 0.0055442325 0.0057472998 0.016716677
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1500 31224.306 0 0.0059295596 0.0059920697 0.0061375228 0.018059152
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1600 31744.535 0 0.0063845142 0.0063600989 0.0064833215 0.019227935
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1700 31472.081 0 0.0068360092 0.0067985824 0.0069464303 0.020581022
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1800 31577.334 0 0.0073001079 0.0071355564 0.0073400543 0.021775719
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1900 31521.234 0 0.0077178677 0.0074371106 0.007708008 0.022862986
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2000 31045.148 0 0.0080515968 0.0078583776 0.0081000219 0.024009996
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2100 31289.809 0 0.0084280175 0.0082322226 0.0084475904 0.02510783
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2200 31505.455 0 0.008802925 0.0085708943 0.0087648194 0.026138639
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2300 31882.722 0 0.0092223105 0.0089242925 0.0092643028 0.027410906
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2400 31028.15 0 0.0095737559 0.0093585981 0.0096771837 0.028609538
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2500 31581.041 0 0.0099316284 0.009785264 0.010100235 0.029817127
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2600 31272.119 0 0.010332986 0.01007291 0.010474606 0.030880502
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2700 31537.8 0 0.010751592 0.010565273 0.01093107 0.032247935
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2800 31060.697 0 0.011156729 0.011010751 0.011260025 0.033427506
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2900 31541.612 0 0.011542003 0.011499419 0.011642873 0.034684295
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3000 31305.382 0 0.011876832 0.011866445 0.012052577 0.035795854
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Loop time of 1.00142 on 4 procs for 3000 steps with 4096 atoms
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Performance: 2588.329 tau/day, 2995.751 timesteps/s
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95.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.084416 | 0.10685 | 0.12695 | 5.7 | 10.67
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Output | 0.001471 | 0.0019466 | 0.0033245 | 1.8 | 0.19
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Modify | 0.66585 | 0.70645 | 0.78995 | 6.0 | 70.54
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Other | | 0.1862 | | | 18.59
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 353.000 ave 353 max 353 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 = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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