211 lines
9.5 KiB
Groff
211 lines
9.5 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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# 3D overdamped active brownian dynamics with no interactions
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variable gamma_t string 3.0
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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}_${fp}
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variable params string 1.0_3.0_${gamma_r}_${fp}
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variable params string 1.0_3.0_1.0_${fp}
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variable params string 1.0_3.0_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 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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1 by 1 by 1 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 = 0.004 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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4096 settings made for dipole/random
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velocity all create 1.0 1 loop geom
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pair_style none
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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 3.0 gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 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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compute press all pressure NULL virial
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thermo_style custom step ke pe 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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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) = 4.362 | 4.362 | 4.362 Mbytes
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Step KinEng PotEng c_press
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0 1.4996338 0 0.068021726
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100 5.184227e+09 0 0.06801544
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200 5.2165482e+09 0 0.068010729
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300 5.2782092e+09 0 0.068009058
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400 5.3244927e+09 0 0.068003481
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500 5.2376606e+09 0 0.067998237
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600 5.2735634e+09 0 0.067998037
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700 5.2692439e+09 0 0.068025402
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800 5.2667984e+09 0 0.068030143
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900 5.242057e+09 0 0.0680246
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1000 5.2557468e+09 0 0.068028348
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1100 5.2975687e+09 0 0.068029528
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1200 5.2081927e+09 0 0.068017542
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1300 5.2636873e+09 0 0.068012572
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1400 5.2187907e+09 0 0.06802049
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1500 5.2349541e+09 0 0.0680373
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1600 5.216092e+09 0 0.068056885
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1700 5.2598019e+09 0 0.068069504
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1800 5.2569065e+09 0 0.068065306
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1900 5.2072055e+09 0 0.068074863
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2000 5.2092961e+09 0 0.068061619
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2100 5.2918572e+09 0 0.068076418
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2200 5.2680626e+09 0 0.068072149
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2300 5.242958e+09 0 0.06806486
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2400 5.2494099e+09 0 0.06805038
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2500 5.2055798e+09 0 0.068072194
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2600 5.2264829e+09 0 0.068069312
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2700 5.3557342e+09 0 0.068064812
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2800 5.2186177e+09 0 0.068042942
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2900 5.2652497e+09 0 0.068044214
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3000 5.1894899e+09 0 0.068044801
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3100 5.241524e+09 0 0.068056675
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3200 5.1915006e+09 0 0.06805641
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3300 5.2367825e+09 0 0.068049946
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3400 5.2288011e+09 0 0.068060182
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3500 5.2704335e+09 0 0.068070881
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3600 5.2886558e+09 0 0.068050439
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3700 5.1976022e+09 0 0.068045927
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3800 5.1525512e+09 0 0.068054494
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3900 5.2212395e+09 0 0.068061432
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4000 5.2309575e+09 0 0.068070842
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4100 5.2260184e+09 0 0.068078378
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4200 5.2829349e+09 0 0.068071652
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4300 5.2204917e+09 0 0.068083072
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4400 5.255242e+09 0 0.068066175
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4500 5.2435681e+09 0 0.068050802
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4600 5.2483356e+09 0 0.06805658
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4700 5.2365098e+09 0 0.068041845
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4800 5.2254325e+09 0 0.068038583
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4900 5.1842852e+09 0 0.068028401
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5000 5.2240722e+09 0 0.068031544
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Loop time of 5.14275 on 1 procs for 5000 steps with 4096 atoms
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Performance: 0.008 tau/day, 972.242 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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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 | 0.26842 | 0.26842 | 0.26842 | 0.0 | 5.22
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Output | 0.0035088 | 0.0035088 | 0.0035088 | 0.0 | 0.07
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Modify | 4.6588 | 4.6588 | 4.6588 | 0.0 | 90.59
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Other | | 0.212 | | | 4.12
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Nlocal: 4096.00 ave 4096 max 4096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 817.000 ave 817 max 817 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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reset_timestep 0
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# MSD to demonstrate expected diffusive behaviour for ideal active
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# brownian motion, which is
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#
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# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
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# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
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#
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# with d being simulation dimension
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compute msd all msd
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thermo_style custom step ke pe 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 12000
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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) = 4.737 | 4.737 | 4.737 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
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0 5.2240722e+09 0 0 0 0 0 0.068031544
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1000 52651.581 0 0.0066842466 0.0067977045 0.0066831353 0.020165086 0.060774985
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2000 52835.806 0 0.013693443 0.014008773 0.013518945 0.041221161 0.094748037
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3000 52097.629 0 0.020666918 0.021696789 0.020665685 0.063029392 0.10673866
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4000 52579.452 0 0.028145318 0.028504548 0.02830967 0.084959536 0.13358122
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5000 51255.456 0 0.035019271 0.034644123 0.03638843 0.10605182 0.13507609
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6000 52730.035 0 0.041412307 0.042689213 0.043339117 0.12744064 0.16497663
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7000 52247.642 0 0.048119396 0.050556395 0.050706527 0.14938232 0.16360301
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8000 52169.849 0 0.055241196 0.058678631 0.059373122 0.17329295 0.1676169
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9000 52520.526 0 0.063519587 0.066592779 0.066988842 0.19710121 0.17142694
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10000 53519.297 0 0.07164814 0.074576535 0.075619236 0.22184391 0.15619444
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11000 52937.293 0 0.077992504 0.083184462 0.082988794 0.24416576 0.15257327
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12000 51762.283 0 0.085959749 0.090992292 0.08984213 0.26679417 0.15996211
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Loop time of 11.6748 on 1 procs for 12000 steps with 4096 atoms
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Performance: 888.063 tau/day, 1027.851 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 | 0.0024164 | 0.0024164 | 0.0024164 | 0.0 | 0.02
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Comm | 0.048127 | 0.048127 | 0.048127 | 0.0 | 0.41
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Output | 0.0019393 | 0.0019393 | 0.0019393 | 0.0 | 0.02
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Modify | 11.12 | 11.12 | 11.12 | 0.0 | 95.24
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Other | | 0.5027 | | | 4.31
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Nlocal: 4096.00 ave 4096 max 4096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 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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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 = 75
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Dangerous builds = 0
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# if you want to check that rotational diffusion is behaving as expected,
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# uncomment next three lines for dump output and then plot <e(t).e(0)>,
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# which should decay exponentially with timescale (d-1)*D_r (with d
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# being simulation dimension)
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#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
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#dump_modify 1 first yes sort id
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#run 120000
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Total wall time: 0:00:16
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