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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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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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) = 5.114 | 5.114 | 5.114 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 34376.187 0 0.00034728749 0.00034318997 0 0.00069047747
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200 36135.708 0 0.00067452936 0.0006818928 0 0.0013564222
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300 34444.929 0 0.0010189319 0.00099849203 0 0.002017424
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400 35668.312 0 0.0013648699 0.0013311884 0 0.0026960583
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500 35388.615 0 0.0017330203 0.0016077184 0 0.0033407387
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600 35180.065 0 0.002052223 0.0019394635 0 0.0039916865
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700 34035.38 0 0.0024329956 0.0022664905 0 0.0046994861
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800 34581.664 0 0.002783885 0.0025794872 0 0.0053633723
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900 34579.945 0 0.003163442 0.0029351952 0 0.0060986372
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1000 34158.066 0 0.0035589034 0.0032627605 0 0.0068216639
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1100 33453.827 0 0.0038861895 0.003565372 0 0.0074515615
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1200 33608.06 0 0.0041325698 0.0038943268 0 0.0080268966
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1300 34381.633 0 0.004405682 0.0043294156 0 0.0087350976
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1400 32925.746 0 0.0047383547 0.0046803517 0 0.0094187065
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1500 34809.764 0 0.0051149571 0.0049309746 0 0.010045932
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1600 33580.096 0 0.0054893472 0.0052465377 0 0.010735885
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1700 34596.275 0 0.00581894 0.0056500316 0 0.011468972
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1800 33926.736 0 0.0062129617 0.0059796125 0 0.012192574
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1900 35577.131 0 0.0065668637 0.0062530163 0 0.01281988
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2000 34224.967 0 0.0070005917 0.006598912 0 0.013599504
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2100 33991.406 0 0.0073134826 0.0069119252 0 0.014225408
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2200 34647.054 0 0.007659301 0.0073434715 0 0.015002772
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2300 33956.835 0 0.007965191 0.0076318537 0 0.015597045
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2400 35272.549 0 0.0082467116 0.007929202 0 0.016175914
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2500 33901.494 0 0.0086251299 0.0082790757 0 0.016904206
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2600 34138.227 0 0.0089419364 0.0086639744 0 0.017605911
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2700 33691.013 0 0.0093083376 0.0090219118 0 0.018330249
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2800 34716.817 0 0.0095840095 0.0094118945 0 0.018995904
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2900 34473.982 0 0.0099773501 0.0098167668 0 0.019794117
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3000 33406.776 0 0.010391969 0.010098625 0 0.020490594
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Loop time of 3.67112 on 1 procs for 3000 steps with 3600 atoms
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Performance: 706.051 tau/day, 817.189 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 | 0.037973 | 0.037973 | 0.037973 | 0.0 | 1.03
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Output | 0.0040674 | 0.0040674 | 0.0040674 | 0.0 | 0.11
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Modify | 3.515 | 3.515 | 3.515 | 0.0 | 95.75
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Other | | 0.1141 | | | 3.11
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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: 0:00:03
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