forked from lijiext/lammps
258 lines
11 KiB
Groff
258 lines
11 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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processors * 1 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 3 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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2 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000491142 secs
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mass * 1.0
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region long block 3 6 0 10 0 10
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set region long type 2
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1400 settings made for type
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velocity all create 1.0 87287
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_coeff * 2 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify every 2 delay 4 check yes
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fix p all property/atom d_WEIGHT
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compute p all property/atom d_WEIGHT
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group fast type 1
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2600 atoms in group fast
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group slow type 2
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1400 atoms in group slow
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balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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rebalancing time: 0.000805378 seconds
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iteration count = 10
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group weights: fast=0.8 slow=2.5
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storing weight in atom property d_WEIGHT
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initial/final max load/proc = 2960 3120
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initial/final imbalance factor = 1.06093 1.11828
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x cuts: 0 0.449707 1
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y cuts: 0 1
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z cuts: 0 1
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variable lastweight atom c_p
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fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT
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variable maximb equal f_0[1]
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variable iter equal f_0[2]
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variable prev equal f_0[3]
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variable final equal f_0
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#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump id all custom 50 dump.lammpstrj id type x y z c_p
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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thermo 50
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run 500
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Per MPI rank memory allocation (min/avg/max) = 4.708 | 4.876 | 5.044 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
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50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
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100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
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150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
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200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
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250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
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300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
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350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
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400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
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450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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Loop time of 5.01752 on 2 procs for 500 steps with 4000 atoms
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Performance: 43049.176 tau/day, 99.651 timesteps/s
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98.5% CPU use with 2 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 | 1.4325 | 2.6317 | 3.8309 | 73.9 | 52.45
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Neigh | 0.72307 | 0.89995 | 1.0768 | 18.6 | 17.94
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Comm | 0.08143 | 1.4587 | 2.836 | 114.0 | 29.07
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Output | 0.00034356 | 0.00034773 | 0.00035191 | 0.0 | 0.01
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Modify | 0.015713 | 0.017661 | 0.01961 | 1.5 | 0.35
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Other | | 0.009141 | | | 0.18
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Nlocal: 2000 ave 2500 max 1500 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10457 ave 11055 max 9859 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 298070 ave 483758 max 112381 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 596139
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Ave neighs/atom = 149.035
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 5.092 | 5.269 | 5.445 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
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600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
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650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
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700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
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750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
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800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
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850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
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900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
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950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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Loop time of 5.38962 on 2 procs for 500 steps with 4000 atoms
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Performance: 40077.052 tau/day, 92.771 timesteps/s
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98.0% CPU use with 2 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 | 0.93627 | 2.5477 | 4.1591 | 101.0 | 47.27
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Neigh | 0.61458 | 0.87078 | 1.127 | 27.5 | 16.16
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Comm | 0.072418 | 1.9424 | 3.8124 | 134.2 | 36.04
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Output | 0.00034833 | 0.00035048 | 0.00035262 | 0.0 | 0.01
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Modify | 0.014652 | 0.018169 | 0.021687 | 2.6 | 0.34
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Other | | 0.01024 | | | 0.19
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Nlocal: 2000 ave 2561 max 1439 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10257 ave 11109 max 9405 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 300836 ave 498670 max 103001 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 601671
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Ave neighs/atom = 150.418
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Neighbor list builds = 51
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Dangerous builds = 0
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balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
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rebalancing time: 0.000744104 seconds
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iteration count = 10
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group weights: fast=0.8 slow=2.5
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storing weight in atom property d_WEIGHT
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initial/final max load/proc = 4428.8 2798.1
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initial/final imbalance factor = 1.58738 1.0029
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x cuts: 0 0.45485 1
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y cuts: 0 1
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z cuts: 0 1
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fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
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run 500
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Per MPI rank memory allocation (min/avg/max) = 5.098 | 5.464 | 5.83 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
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1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
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1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
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1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
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1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
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1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
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1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
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1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
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1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137
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1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
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Loop time of 5.50675 on 2 procs for 500 steps with 4000 atoms
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Performance: 39224.584 tau/day, 90.798 timesteps/s
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98.0% CPU use with 2 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 | 1.1091 | 2.6165 | 4.124 | 93.2 | 47.51
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Neigh | 0.49666 | 0.88338 | 1.2701 | 41.1 | 16.04
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Comm | 0.079062 | 1.9768 | 3.8745 | 135.0 | 35.90
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Output | 0.00032926 | 0.00041151 | 0.00049376 | 0.0 | 0.01
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Modify | 0.012776 | 0.018102 | 0.023428 | 4.0 | 0.33
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Other | | 0.01156 | | | 0.21
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Nlocal: 2000 ave 3010 max 990 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10343 ave 12129 max 8557 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 302958 ave 519016 max 86901 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 605917
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Ave neighs/atom = 151.479
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 5.847 | 5.872 | 5.897 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
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1550 0.5371361 -6.250403 0 -5.4449003 -1.7647032 4738.2137
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1600 0.54679571 -6.2646443 0 -5.4446558 -1.8115722 4738.2137
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1650 0.53806587 -6.2519009 0 -5.4450039 -1.7409152 4738.2137
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1700 0.53479436 -6.2469032 0 -5.4449122 -1.7162441 4738.2137
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1750 0.53714071 -6.2506513 0 -5.4451416 -1.7340205 4738.2137
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1800 0.52750533 -6.2358819 0 -5.4448217 -1.687537 4738.2137
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1850 0.54585346 -6.262937 0 -5.4443615 -1.7758597 4738.2137
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1900 0.53011247 -6.2387653 0 -5.4437954 -1.6382086 4738.2137
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1950 0.54287683 -6.2583097 0 -5.4441981 -1.7367469 4738.2137
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2000 0.52771288 -6.2349676 0 -5.4435962 -1.5593804 4738.2137
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Loop time of 5.80884 on 2 procs for 500 steps with 4000 atoms
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Performance: 37184.695 tau/day, 86.076 timesteps/s
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97.7% CPU use with 2 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 | 0.71314 | 2.5435 | 4.3738 | 114.8 | 43.79
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Neigh | 0.39935 | 0.85806 | 1.3168 | 49.5 | 14.77
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Comm | 0.082629 | 2.3761 | 4.6695 | 148.8 | 40.90
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Output | 0.00034571 | 0.00044024 | 0.00053477 | 0.0 | 0.01
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Modify | 0.011643 | 0.018227 | 0.024811 | 4.9 | 0.31
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Other | | 0.01257 | | | 0.22
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Nlocal: 2000 ave 3032 max 968 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10266 ave 12245 max 8287 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 303998 ave 525128 max 82868 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 607996
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Ave neighs/atom = 151.999
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Neighbor list builds = 51
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Dangerous builds = 0
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Total wall time: 0:00:21
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