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 2D #####
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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 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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1 by 1 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 = 0.005 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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3600 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}_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) = 4.664 | 4.664 | 4.664 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 20867.136 0 0.00040006704 0.00039570887 0 0.00079577592
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200 20835.491 0 0.00077560901 0.00080455484 0 0.0015801638
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300 20813.122 0 0.0011737739 0.0012172689 0 0.0023910428
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400 21137.397 0 0.0015587675 0.0016096093 0 0.0031683768
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500 21167.188 0 0.0019294105 0.0020251322 0 0.0039545428
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600 21345.908 0 0.0023105313 0.0024111742 0 0.0047217054
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700 21086.272 0 0.0027236116 0.0027846006 0 0.0055082122
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800 20840.906 0 0.0031505299 0.0031810732 0 0.0063316031
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900 20916.456 0 0.0035525852 0.0035981301 0 0.0071507153
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1000 20752.249 0 0.0039147929 0.0039791172 0 0.0078939101
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1100 20643.612 0 0.0042977921 0.0043701484 0 0.0086679405
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1200 21085.63 0 0.0045584242 0.0047475091 0 0.0093059332
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1300 20900.794 0 0.0049718803 0.0051481706 0 0.010120051
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1400 20980.731 0 0.0054234603 0.0054230724 0 0.010846533
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1500 20916.308 0 0.0058502946 0.0058114313 0 0.011661726
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1600 20949.786 0 0.0062258463 0.006208129 0 0.012433975
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1700 20531.205 0 0.0066276219 0.006595921 0 0.013223543
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1800 21418.472 0 0.0070077409 0.007030461 0 0.014038202
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1900 21291.928 0 0.0074052208 0.0074333041 0 0.014838525
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2000 20893.895 0 0.0077407477 0.007901402 0 0.01564215
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2100 21218.001 0 0.0080384756 0.0082611258 0 0.016299601
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2200 21116.189 0 0.0084325164 0.008617977 0 0.017050493
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2300 20718.83 0 0.0089455345 0.0091768161 0 0.018122351
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2400 20719.164 0 0.0093666455 0.0095272546 0 0.0188939
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2500 20991.382 0 0.009706795 0.0098256506 0 0.019532446
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2600 20515.74 0 0.0099247069 0.010329841 0 0.020254548
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2700 21001.55 0 0.010448354 0.010693502 0 0.021141855
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2800 21363.824 0 0.010990971 0.011142092 0 0.022133063
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2900 20497.025 0 0.011399704 0.011504868 0 0.022904573
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3000 20726.572 0 0.011785354 0.01187482 0 0.023660175
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Loop time of 1.76023 on 1 procs for 3000 steps with 3600 atoms
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Performance: 1472.538 tau/day, 1704.326 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 | 0.026518 | 0.026518 | 0.026518 | 0.0 | 1.51
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Output | 0.0040107 | 0.0040107 | 0.0040107 | 0.0 | 0.23
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Modify | 1.6194 | 1.6194 | 1.6194 | 0.0 | 92.00
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Other | | 0.1103 | | | 6.27
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Nlocal: 3600.00 ave 3600 max 3600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 121.000 ave 121 max 121 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: 0:00:01
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