152 lines
6.2 KiB
Groff
152 lines
6.2 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
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variable gamma_t equal 1.0
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variable temp equal 1.0
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variable seed equal 1974019
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variable fp equal 4.0
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variable params string ${gamma_t}_${temp}_${fp}
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variable params string 1_${temp}_${fp}
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variable params string 1_1_${fp}
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variable params string 1_1_4
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units lj
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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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1 by 1 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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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 step all brownian ${temp} ${seed} gamma_t ${gamma_t}
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fix step all brownian 1 ${seed} gamma_t ${gamma_t}
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fix step all brownian 1 1974019 gamma_t ${gamma_t}
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fix step all brownian 1 1974019 gamma_t 1
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fix vel all propel/self velocity ${fp}
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fix vel all propel/self velocity 4
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fix 2 all enforce2d
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fix_modify vel virial yes
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compute press all pressure NULL virial
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thermo_style custom step temp epair c_press
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#equilibration
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timestep 0.0000000001
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thermo 500
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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) = 2.289 | 2.289 | 2.289 Mbytes
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Step Temp E_pair c_press
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0 1 0 -0.18336111
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500 2.0519273e+10 0 -0.048238222
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1000 1.9821717e+10 0 -0.4711053
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1500 1.9697609e+10 0 -0.13539588
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2000 2.0209443e+10 0 0.0094958039
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2500 1.9591299e+10 0 0.40117118
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3000 2.089566e+10 0 -0.036548251
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3500 1.978692e+10 0 0.28282578
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4000 2.0657848e+10 0 0.17618064
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4500 2.0837353e+10 0 -0.080724651
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5000 2.0348316e+10 0 -0.17471195
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Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms
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Performance: 0.075 tau/day, 8693.168 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 | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64
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Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
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Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41
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Other | | 0.05121 | | | 8.90
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 65.0000 ave 65 max 65 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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#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[*] 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) = 2.664 | 2.664 | 2.664 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 2.0328444e+10 0 0 0 0 0 -0.17471195
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1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807
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2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929
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3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039
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4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117
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5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406
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6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034
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7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674
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8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569
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9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407
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10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211
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11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437
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12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034
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Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms
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Performance: 7542.303 tau/day, 8729.517 timesteps/s
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99.8% 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 | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01
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Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18
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Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05
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Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78
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Other | | 0.1235 | | | 8.98
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Nlocal: 1024.00 ave 1024 max 1024 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 = 15
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Dangerous builds = 0
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Total wall time: 0:00:01
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