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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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 = 0.002 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) = 2.694 | 2.694 | 2.694 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 1500286.3 0 0.0098123603 0.010352169 0.010242435 0.030406964
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200 1488308 0 0.019934427 0.019968198 0.020471735 0.06037436
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300 1484472.4 0 0.029397156 0.030749312 0.030121294 0.090267762
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400 1517938.7 0 0.039217504 0.041440617 0.040512943 0.12117106
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500 1492769.5 0 0.04890343 0.051561801 0.050614941 0.15108017
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600 1510159.6 0 0.059770181 0.061650364 0.061298117 0.18271866
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700 1485424.1 0 0.070537955 0.071144877 0.071141546 0.21282438
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800 1496377.2 0 0.081291995 0.082546059 0.080653381 0.24449144
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900 1484409.1 0 0.090940427 0.093298981 0.091328056 0.27556746
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1000 1503322.4 0 0.10176921 0.10246052 0.10151773 0.30574747
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1100 1503322.4 0 0.11295993 0.11052632 0.11053406 0.33402031
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1200 1489236.2 0 0.12509723 0.11961982 0.12146498 0.36618203
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1300 1476050.3 0 0.13449034 0.12941323 0.1309765 0.39488007
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1400 1520818.7 0 0.14613571 0.13788044 0.14083944 0.42485558
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1500 1498936.4 0 0.15752286 0.15057712 0.15063399 0.45873397
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1600 1507524.1 0 0.16793678 0.16095681 0.16063531 0.4895289
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1700 1480581.2 0 0.17748019 0.172614 0.16922383 0.51931802
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1800 1505353.6 0 0.18850931 0.18304171 0.18063119 0.55218221
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1900 1491234.7 0 0.19836402 0.19306339 0.1929707 0.58439811
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2000 1519868.8 0 0.20698191 0.20211344 0.20328302 0.61237838
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2100 1493919.5 0 0.21453524 0.21186097 0.21423293 0.64062914
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2200 1517098.6 0 0.2257338 0.22381647 0.22474081 0.67429108
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2300 1481270.7 0 0.23499747 0.23348379 0.23498244 0.70346369
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2400 1495445.1 0 0.24535894 0.24290239 0.24229161 0.73055293
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2500 1522839.3 0 0.25695938 0.25109669 0.25214541 0.76020148
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2600 1518697.4 0 0.26680819 0.26120216 0.2604112 0.78842155
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2700 1529283.1 0 0.27524422 0.26942681 0.27148042 0.81615146
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2800 1500557.5 0 0.28436226 0.27957592 0.27935619 0.84329437
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2900 1509711.1 0 0.2948528 0.28562401 0.29055956 0.87103637
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3000 1522712.8 0 0.30347033 0.2975063 0.30121685 0.90219348
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Loop time of 2.35056 on 1 procs for 3000 steps with 4096 atoms
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Performance: 1102.718 tau/day, 1276.293 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 | 0.00077772 | 0.00077772 | 0.00077772 | 0.0 | 0.03
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Comm | 0.010985 | 0.010985 | 0.010985 | 0.0 | 0.47
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Output | 0.0045807 | 0.0045807 | 0.0045807 | 0.0 | 0.19
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Modify | 2.2116 | 2.2116 | 2.2116 | 0.0 | 94.09
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Other | | 0.1226 | | | 5.22
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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 = 24
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Dangerous builds = 0
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Total wall time: 0:00:02
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