222 lines
9.9 KiB
Groff
222 lines
9.9 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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# 2D overdamped active brownian particle dynamics (ABP)
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# with WCA potential
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variable gamma_t string 1.0
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variable gamma_r string 1.0
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variable temp string 1.0
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variable seed equal 1974019
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variable fp string 4.0
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variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
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variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
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variable params string 1.0_1.0_${gamma_r}_${fp}
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variable params string 1.0_1.0_1.0_${fp}
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variable params string 1.0_1.0_1.0_4.0
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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 -16 16 -16 16 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 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 1024 atoms
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create_atoms CPU = 0.001 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 1974019 1.0
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Setting atom values ...
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1024 settings made for dipole/random
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velocity all create 1.0 1 loop geom
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# more careful with neighbors since higher diffusion in abps
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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# WCA potential (purely repulsive)
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 1.1224
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pair_modify shift yes
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# overdamped brownian dynamics time-step
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fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
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# self-propulsion force along the dipole direction
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fix activity all propel/self dipole ${fp}
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fix activity all propel/self dipole 4.0
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fix 2 all enforce2d
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compute press all pressure NULL virial
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thermo_style custom step pe ke c_press
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#equilibration
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timestep 0.0000000001
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thermo 100
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 1 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.1224
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ghost atom cutoff = 2.1224
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binsize = 1.0612, bins = 48 48 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: half/bin/2d/newtoff
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes
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Step PotEng KinEng c_press
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0 0 0.99902344 -0.53979198
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100 0 1.0503521e+10 -0.53983092
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200 0 1.0390343e+10 -0.5398287
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300 0 1.0493441e+10 -0.53979247
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400 0 1.0545991e+10 -0.53978678
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500 0 1.0266398e+10 -0.53986297
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600 0 1.0484775e+10 -0.53978746
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700 0 1.0583596e+10 -0.53969114
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800 0 1.0521919e+10 -0.53968754
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900 0 1.0492019e+10 -0.53958643
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1000 0 1.0298052e+10 -0.53949872
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1100 0 1.0531424e+10 -0.53955431
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1200 0 1.0635635e+10 -0.53960048
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1300 0 1.0633405e+10 -0.53966331
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1400 0 1.0195401e+10 -0.53968849
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1500 0 1.0593758e+10 -0.53969763
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1600 0 1.0425238e+10 -0.53971936
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1700 0 1.0470017e+10 -0.53981957
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1800 0 1.0545953e+10 -0.53987747
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1900 0 1.0425015e+10 -0.53990412
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2000 0 1.0655092e+10 -0.5399511
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2100 0 1.0197224e+10 -0.53988687
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2200 0 1.0448012e+10 -0.53986066
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2300 0 1.0355268e+10 -0.53980415
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2400 0 1.0246979e+10 -0.53979737
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2500 0 1.0021539e+10 -0.5397919
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2600 0 1.0200824e+10 -0.5397575
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2700 0 1.0721591e+10 -0.53973512
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2800 0 1.0354562e+10 -0.5397127
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2900 0 1.0306795e+10 -0.5396946
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3000 0 1.0301339e+10 -0.53968642
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3100 0 1.0435826e+10 -0.53970945
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3200 0 1.019524e+10 -0.53969746
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3300 0 1.0550481e+10 -0.53967977
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3400 0 1.0283446e+10 -0.53971102
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3500 0 1.0956695e+10 -0.53976173
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3600 0 1.0271033e+10 -0.53983632
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3700 0 1.0389461e+10 -0.53977293
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3800 0 1.0680515e+10 -0.53977425
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3900 0 1.0072183e+10 -0.53982922
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4000 0 1.0458036e+10 -0.53980042
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4100 0 1.0588689e+10 -0.53971405
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4200 0 1.0068308e+10 -0.5398033
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4300 0 1.0502064e+10 -0.53981291
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4400 0 1.0590544e+10 -0.5398346
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4500 0 1.0411612e+10 -0.5397916
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4600 0 1.0518596e+10 -0.53984868
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4700 0 1.0386105e+10 -0.53977803
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4800 0 1.029525e+10 -0.53970882
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4900 0 1.0519112e+10 -0.53969616
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5000 0 1.0335841e+10 -0.53976477
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Loop time of 0.471663 on 4 procs for 5000 steps with 1024 atoms
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Performance: 0.092 tau/day, 10600.781 timesteps/s
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95.8% 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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Pair | 0.067099 | 0.07105 | 0.077898 | 1.6 | 15.06
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0581 | 0.066084 | 0.072322 | 2.0 | 14.01
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Output | 0.0014644 | 0.002618 | 0.0037239 | 1.6 | 0.56
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Modify | 0.24817 | 0.25719 | 0.26697 | 1.3 | 54.53
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Other | | 0.07472 | | | 15.84
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 105.000 ave 105 max 105 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 544.000 ave 544 max 544 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2176
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Ave neighs/atom = 2.1250000
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Neighbor list builds = 0
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Dangerous builds = 0
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reset_timestep 0
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# MSD
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compute msd all msd
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thermo_style custom step temp epair c_msd[*] c_press
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timestep 0.00001
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thermo 1000
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# main run
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run 20000
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Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes
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Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
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0 1.0345945e+10 0 0 0 0 0 -0.53976477
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1000 100114.28 0.0029703577 0.020320684 0.020950989 0 0.041271673 -0.43948247
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2000 106825.83 0.020969054 0.039616412 0.039459167 0 0.079075578 -0.22765541
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3000 105287.4 0.037343571 0.056828177 0.058639835 0 0.11546801 -0.11728136
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4000 104522.23 0.052237136 0.080264931 0.080863543 0 0.16112847 0.033230576
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5000 103277.94 0.053791862 0.099188864 0.10141444 0 0.20060331 0.073591503
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6000 104252.87 0.073304776 0.11964238 0.1215576 0 0.24119999 0.22062305
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7000 105184.19 0.089054043 0.13691291 0.14216478 0 0.27907769 0.29015692
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8000 104211.82 0.072577918 0.15820522 0.15658491 0 0.31479013 0.25908291
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9000 99242.172 0.071616004 0.17658708 0.17479704 0 0.35138412 0.26305532
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10000 105070.83 0.077009979 0.20175025 0.19871513 0 0.40046538 0.34120567
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11000 106421.07 0.098623061 0.22472634 0.22671582 0 0.45144216 0.44021335
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12000 103209.85 0.12032847 0.25004966 0.25368441 0 0.50373406 0.57344873
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13000 107156.89 0.1058386 0.27283231 0.2744873 0 0.54731961 0.47957408
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14000 108119.3 0.1204768 0.29333677 0.30054535 0 0.59388213 0.51832639
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15000 105477.62 0.12510026 0.32217621 0.32806599 0 0.6502422 0.50174158
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16000 106676.27 0.10893618 0.34980866 0.36031184 0 0.7101205 0.44769198
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17000 103048.41 0.10625673 0.3781797 0.37970499 0 0.75788468 0.42803898
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18000 109454.8 0.10555778 0.40997694 0.41396777 0 0.82394471 0.41380982
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19000 107459.73 0.11267582 0.43757738 0.43577856 0 0.87335594 0.4917748
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20000 101991.9 0.084279008 0.45363612 0.46278076 0 0.91641688 0.41707912
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Loop time of 1.80877 on 4 procs for 20000 steps with 1024 atoms
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Performance: 9553.439 tau/day, 11057.221 timesteps/s
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98.5% 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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Pair | 0.34461 | 0.36424 | 0.40948 | 4.4 | 20.14
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Neigh | 0.0031493 | 0.003215 | 0.0032432 | 0.1 | 0.18
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Comm | 0.19538 | 0.20419 | 0.2104 | 1.2 | 11.29
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Output | 0.00054121 | 0.00087297 | 0.0018425 | 0.0 | 0.05
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Modify | 0.98335 | 1.0156 | 1.0791 | 3.8 | 56.15
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Other | | 0.2207 | | | 12.20
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Nlocal: 256.000 ave 261 max 252 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Nghost: 93.0000 ave 100 max 83 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Neighs: 662.250 ave 693 max 635 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Total # of neighbors = 2649
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Ave neighs/atom = 2.5869141
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Neighbor list builds = 23
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Dangerous builds = 0
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Total wall time: 0:00:02
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