120 lines
5.7 KiB
Groff
120 lines
5.7 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### overdamped dynamics of non-interacting point particles in 3D #####
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variable rng string gaussian
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variable seed string 198098
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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variable params string gaussian_${temp}_${gamma_t}
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variable params string gaussian_5.0_${gamma_t}
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variable params string gaussian_5.0_1.0
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units lj
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atom_style atomic
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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 = 0.001 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 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 100
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# main run
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run 3000
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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) = 2.672 | 2.672 | 2.672 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
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0 1.4996338 0 0 0 0 0
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100 1515328.2 0 0.010465453 0.010044629 0.0097242319 0.030234314
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200 1510820.8 0 0.020658886 0.019954762 0.020008864 0.060622512
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300 1482006.5 0 0.030402195 0.029802874 0.030047586 0.090252655
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400 1492228.5 0 0.039622543 0.038899144 0.040381854 0.11890354
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500 1494985.5 0 0.050523465 0.050022913 0.050186478 0.15073286
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600 1516047.4 0 0.061111845 0.061433818 0.059195364 0.18174103
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700 1510021.8 0 0.071636778 0.072829755 0.06946406 0.21393059
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800 1505964.7 0 0.08240965 0.08433785 0.078799851 0.24554735
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900 1491035.9 0 0.093659937 0.094517749 0.08812559 0.27630328
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1000 1516599.6 0 0.10436496 0.10431759 0.097480868 0.30616342
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1100 1495170.3 0 0.11468757 0.111397 0.1069763 0.33306087
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1200 1500630.6 0 0.12360977 0.12264534 0.11583999 0.3620951
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1300 1474889.5 0 0.13432447 0.13471694 0.12702491 0.39606632
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1400 1487145.8 0 0.14573239 0.14431493 0.13669403 0.42674135
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1500 1519496.7 0 0.15610742 0.15505416 0.14600182 0.4571634
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1600 1525674.1 0 0.16728653 0.1649354 0.15562133 0.48784325
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1700 1540725.4 0 0.17846447 0.17666562 0.16531781 0.52044791
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1800 1512334.8 0 0.18872753 0.18538847 0.17450009 0.54861609
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1900 1498371.4 0 0.19688928 0.19333299 0.18581712 0.5760394
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2000 1546459.4 0 0.20955053 0.20243854 0.19613897 0.60812803
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2100 1509712.9 0 0.21922567 0.20940597 0.20567239 0.63430404
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2200 1509630.4 0 0.23067999 0.21856734 0.21619911 0.66544645
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2300 1483929.1 0 0.24160803 0.231048 0.22617193 0.69882797
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2400 1488492.1 0 0.25399491 0.24082678 0.23972356 0.73454526
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2500 1508107.9 0 0.26608734 0.25316913 0.2486814 0.76793787
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2600 1511952.1 0 0.27523956 0.2623673 0.25706539 0.79467225
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2700 1488888.8 0 0.28518299 0.27425585 0.26728622 0.82672506
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2800 1515428.4 0 0.29595429 0.28589969 0.27781327 0.85966725
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2900 1504312.1 0 0.30393798 0.29533034 0.28725362 0.88652194
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3000 1521521.3 0 0.31445132 0.30117607 0.29959324 0.91522062
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Loop time of 0.708196 on 4 procs for 3000 steps with 4096 atoms
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Performance: 3660.004 tau/day, 4236.115 timesteps/s
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97.2% 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 | 0.00020647 | 0.00021023 | 0.0002141 | 0.0 | 0.03
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Comm | 0.0045607 | 0.0050649 | 0.0053098 | 0.4 | 0.72
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Output | 0.0013759 | 0.002265 | 0.0037355 | 1.9 | 0.32
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Modify | 0.57353 | 0.58931 | 0.6109 | 1.8 | 83.21
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Other | | 0.1113 | | | 15.72
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Nlocal: 1024.00 ave 1043 max 1001 min
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Histogram: 1 0 0 0 0 2 0 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 = 25
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Dangerous builds = 0
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Total wall time: 0:00:00
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