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 2D #####
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variable rng string gaussian
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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 inf
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variable gamma_r_2 string inf
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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 inf
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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 gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
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variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
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variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
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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 2
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newton off
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lattice sq 0.4
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Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
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region box block -30 30 -30 30 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
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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 3600 atoms
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create_atoms CPU = 0.007 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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3600 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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3600 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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3600 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 gaussian 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 gaussian gamma_r_eigen inf ${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 gaussian gamma_r_eigen inf inf ${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 gaussian gamma_r_eigen inf inf 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 gaussian gamma_r_eigen inf inf 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 gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
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fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${params}_2d.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) = 5.102 | 5.102 | 5.102 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 0.99972222 0 0 0 0 0
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100 33874.438 0 0.0003458147 0.00033165629 0 0.00067747099
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200 34893.188 0 0.00066290209 0.00068146332 0 0.0013443654
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300 34494.226 0 0.0010064902 0.0010276646 0 0.0020341548
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400 34537.887 0 0.0013457339 0.0014057042 0 0.0027514381
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500 34458.46 0 0.0017006949 0.0017120083 0 0.0034127033
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600 33229.977 0 0.0020841613 0.0020485346 0 0.0041326959
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700 33288.631 0 0.0024270272 0.0023673304 0 0.0047943576
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800 35317.512 0 0.0027924435 0.0026950912 0 0.0054875347
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900 33094.299 0 0.0031503627 0.0030789319 0 0.0062292946
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1000 35801.751 0 0.003489398 0.0034594626 0 0.0069488607
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1100 33427.701 0 0.0038547506 0.0038375809 0 0.0076923316
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1200 34675.07 0 0.0041824195 0.0042017298 0 0.0083841493
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1300 33080.294 0 0.0045258945 0.0045816356 0 0.0091075301
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1400 34927.288 0 0.0048252992 0.0049215701 0 0.0097468693
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1500 34338.558 0 0.0051959155 0.0053020102 0 0.010497926
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1600 34686.248 0 0.0055111463 0.0056220225 0 0.011133169
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1700 34336.158 0 0.0059240394 0.0059060319 0 0.011830071
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1800 34315.859 0 0.0063027944 0.0063004467 0 0.012603241
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1900 35096.721 0 0.0066098525 0.00672222 0 0.013332073
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2000 33544.18 0 0.0069401261 0.007074124 0 0.01401425
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2100 33863.219 0 0.0072726502 0.0074175954 0 0.014690246
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2200 34705.892 0 0.0075586722 0.0077552683 0 0.015313941
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2300 34025.357 0 0.0079046728 0.0081760519 0 0.016080725
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2400 34741.849 0 0.008252969 0.0085203087 0 0.016773278
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2500 34406.959 0 0.0085370091 0.0088556377 0 0.017392647
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2600 34062.63 0 0.0088134153 0.0092536326 0 0.018067048
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2700 34677.666 0 0.0090592854 0.0096225881 0 0.018681874
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2800 33464.216 0 0.0093984162 0.0099647695 0 0.019363186
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2900 32920.721 0 0.0098222985 0.010366517 0 0.020188816
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3000 34539.66 0 0.010133317 0.01068102 0 0.020814337
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Loop time of 1.12143 on 4 procs for 3000 steps with 3600 atoms
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Performance: 2311.341 tau/day, 2675.163 timesteps/s
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96.1% 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 | 0.036017 | 0.042828 | 0.051558 | 2.7 | 3.82
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Output | 0.0012608 | 0.0025993 | 0.0063775 | 4.3 | 0.23
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Modify | 0.9002 | 0.93095 | 0.99546 | 3.9 | 83.01
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Other | | 0.1451 | | | 12.93
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Nlocal: 900.000 ave 900 max 900 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 61.0000 ave 61 max 61 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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