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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2 by 1 by 2 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 = 0.002 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) = 4.319 | 4.319 | 4.319 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 5.2484581e+09 0 0.068010768
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200 5.277936e+09 0 0.068024039
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300 5.2651427e+09 0 0.068014821
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400 5.2066432e+09 0 0.068027583
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500 5.2250276e+09 0 0.068030242
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600 5.239771e+09 0 0.068018406
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700 5.1953674e+09 0 0.068017081
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800 5.2097107e+09 0 0.068010167
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900 5.2559863e+09 0 0.068012923
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1000 5.2743197e+09 0 0.068017855
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1100 5.1999741e+09 0 0.068014189
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1200 5.3216344e+09 0 0.068005604
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1300 5.2839264e+09 0 0.067982558
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1400 5.2462761e+09 0 0.067977843
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1500 5.2208208e+09 0 0.067979594
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1600 5.2740284e+09 0 0.067972573
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1700 5.1919692e+09 0 0.067974452
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1800 5.2497614e+09 0 0.067966417
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1900 5.2910442e+09 0 0.067976096
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2000 5.27238e+09 0 0.067963979
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2100 5.3305398e+09 0 0.06795661
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2200 5.205471e+09 0 0.067970212
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2300 5.1803713e+09 0 0.067931775
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2400 5.2134311e+09 0 0.067941825
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2500 5.2367424e+09 0 0.067963456
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2600 5.2246738e+09 0 0.067957556
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2700 5.2514573e+09 0 0.067960724
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2800 5.2601577e+09 0 0.067965167
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2900 5.2422855e+09 0 0.067956561
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3000 5.1796674e+09 0 0.067946764
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3100 5.2308189e+09 0 0.067946585
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3200 5.1835395e+09 0 0.067951909
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3300 5.2762112e+09 0 0.067963199
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3400 5.3224133e+09 0 0.067944918
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3500 5.2314242e+09 0 0.06795318
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3600 5.2760337e+09 0 0.067958005
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3700 5.2549349e+09 0 0.06795228
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3800 5.3343065e+09 0 0.067944561
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3900 5.2440993e+09 0 0.067947433
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4000 5.2565026e+09 0 0.067962624
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4100 5.1766738e+09 0 0.067949542
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4200 5.2058437e+09 0 0.067959946
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4300 5.2777775e+09 0 0.067945883
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4400 5.2020331e+09 0 0.067953495
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4500 5.1417619e+09 0 0.067944161
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4600 5.2672994e+09 0 0.067936777
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4700 5.222847e+09 0 0.067943025
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4800 5.2467842e+09 0 0.06794191
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4900 5.2784378e+09 0 0.067939495
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5000 5.2563969e+09 0 0.067940246
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Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms
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Performance: 0.028 tau/day, 3208.260 timesteps/s
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97.1% 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 | 0.15304 | 0.15677 | 0.16459 | 1.2 | 10.06
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Output | 0.0012078 | 0.0021182 | 0.0047011 | 3.2 | 0.14
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Modify | 1.1966 | 1.2236 | 1.2761 | 2.8 | 78.51
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Other | | 0.176 | | | 11.29
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 353.000 ave 353 max 353 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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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) = 4.694 | 4.694 | 4.694 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 5.2563969e+09 0 0 0 0 0 0.067940246
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1000 52568.549 0 0.0067249858 0.0066478843 0.0066014231 0.019974293 0.066777589
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2000 52836.937 0 0.013611101 0.013799663 0.013161144 0.040571907 0.066769693
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3000 52129.467 0 0.020360834 0.02089829 0.01995025 0.061209374 0.060026879
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4000 52075.177 0 0.027638751 0.028062314 0.026895904 0.082596969 0.078290387
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5000 52203.996 0 0.034087112 0.034933104 0.033832559 0.10285278 0.083657551
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6000 52986.764 0 0.041562413 0.042238976 0.040542538 0.12434393 0.11542014
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7000 51941.229 0 0.049216989 0.049250201 0.047598008 0.1460652 0.13739893
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8000 52618.713 0 0.057198947 0.057409217 0.05404895 0.16865711 0.13681938
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9000 52501.332 0 0.066447829 0.065262287 0.062271789 0.19398191 0.14306596
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10000 52545.628 0 0.073800792 0.072510553 0.070100713 0.21641206 0.14689578
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11000 52416.561 0 0.081881868 0.080638809 0.078969817 0.24149049 0.15608324
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12000 52271.578 0 0.090521937 0.088555992 0.08592156 0.26499949 0.1474981
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Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms
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Performance: 3307.113 tau/day, 3827.677 timesteps/s
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99.2% 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 | 0.00060225 | 0.00060934 | 0.00061345 | 0.0 | 0.02
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Comm | 0.029197 | 0.029376 | 0.029582 | 0.1 | 0.94
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Output | 0.00060606 | 0.00087148 | 0.0016448 | 0.0 | 0.03
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Modify | 2.84 | 2.8773 | 2.8942 | 1.3 | 91.78
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Other | | 0.2269 | | | 7.24
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Nlocal: 1024.00 ave 1037 max 999 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Nghost: 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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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 = 73
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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: 0:00:04
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