152 lines
6.3 KiB
Groff
152 lines
6.3 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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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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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 1.9862591e+10 0 -0.32013566
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1000 2.0093184e+10 0 -0.36609742
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1500 1.9562283e+10 0 -0.53349351
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2000 1.9903977e+10 0 0.63783249
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2500 2.0260128e+10 0 0.30046413
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3000 1.9948065e+10 0 -0.63093105
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3500 1.9507486e+10 0 0.48762848
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4000 2.0049087e+10 0 0.40289309
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4500 1.9975813e+10 0 0.57649363
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5000 2.0129291e+10 0 -0.41288352
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Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
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Performance: 0.181 tau/day, 20924.952 timesteps/s
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92.6% 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 | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
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Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
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Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
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Other | | 0.06992 | | | 29.26
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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: 33.0000 ave 33 max 33 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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#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 2.0109634e+10 0 0 0 0 0 -0.41288352
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1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
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2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
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3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
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4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
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5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
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6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
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7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
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8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
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9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
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10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
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11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031
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12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052
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Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms
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Performance: 23402.683 tau/day, 27086.439 timesteps/s
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97.7% 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 | 0 | 0 | 0.0 | 0.00
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Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01
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Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69
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Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12
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Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33
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Other | | 0.1057 | | | 23.86
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Nlocal: 256.000 ave 259 max 253 min
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Histogram: 1 0 0 1 0 0 1 0 0 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 = 15
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Dangerous builds = 0
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Total wall time: 0:00:00
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