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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4 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 = 0.000424862 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: 0.00115108 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 = 2160 1620
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initial/final imbalance factor = 1.54839 1.16129
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x cuts: 0 0.300049 0.449951 0.599854 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) = 4.132 | 4.192 | 4.274 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 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
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100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
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150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
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200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
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250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
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300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
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350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
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400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
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450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
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500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
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Loop time of 2.66424 on 4 procs for 500 steps with 4000 atoms
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Performance: 81073.650 tau/day, 187.670 timesteps/s
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97.3% 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 | 1.1083 | 1.3909 | 1.7318 | 24.2 | 52.21
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Neigh | 0.19732 | 0.45425 | 0.7722 | 38.2 | 17.05
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Comm | 0.24921 | 0.79627 | 1.3351 | 60.3 | 29.89
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Output | 0.00041294 | 0.00065368 | 0.0011899 | 0.0 | 0.02
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Modify | 0.0071657 | 0.010935 | 0.015748 | 3.6 | 0.41
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Other | | 0.01124 | | | 0.42
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Nlocal: 1000 ave 1870 max 299 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 8679.25 ave 10190 max 7374 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 149308 ave 215125 max 81132 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 597231
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Ave neighs/atom = 149.308
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Neighbor list builds = 50
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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) = 4.134 | 4.387 | 4.664 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
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550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
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600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
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650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
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700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
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750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
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800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
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850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
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900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
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950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
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1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
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Loop time of 3.02509 on 4 procs for 500 steps with 4000 atoms
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Performance: 71402.836 tau/day, 165.284 timesteps/s
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96.7% 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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---------------------------------------------------------------
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Pair | 0.6808 | 1.3385 | 1.959 | 52.5 | 44.25
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Neigh | 0.13127 | 0.4678 | 0.86924 | 48.5 | 15.46
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Comm | 0.19735 | 1.1921 | 2.1903 | 85.9 | 39.41
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Output | 0.00045371 | 0.00090569 | 0.0013952 | 0.0 | 0.03
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Modify | 0.0062041 | 0.011167 | 0.01691 | 4.5 | 0.37
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Other | | 0.01462 | | | 0.48
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Nlocal: 1000 ave 1935 max 262 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 8739.75 ave 10498 max 7333 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 150170 ave 231608 max 72161 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 600678
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Ave neighs/atom = 150.169
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Neighbor list builds = 53
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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: 0.000575304 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 = 2318.1 1408.1
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initial/final imbalance factor = 1.66172 1.00939
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x cuts: 0 0.337054 0.454419 0.59556 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) = 4.136 | 4.393 | 4.673 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
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1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
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1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
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1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
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1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
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1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
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1300 0.54134321 -6.2590728 0 -5.447261 -1.917027 4738.2137
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1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
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1400 0.53726925 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
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1450 0.54525929 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
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1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137
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Loop time of 3.07108 on 4 procs for 500 steps with 4000 atoms
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Performance: 70333.514 tau/day, 162.809 timesteps/s
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96.8% 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 | 0.77463 | 1.3897 | 2.1328 | 51.3 | 45.25
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Neigh | 0.13416 | 0.45546 | 0.80534 | 46.9 | 14.83
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Comm | 0.17763 | 1.2036 | 2.1448 | 83.6 | 39.19
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Output | 0.00039482 | 0.00067067 | 0.0013118 | 0.0 | 0.02
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Modify | 0.0058403 | 0.010695 | 0.015841 | 4.5 | 0.35
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Other | | 0.01099 | | | 0.36
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Nlocal: 1000 ave 1955 max 199 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 8729 ave 10472 max 7399 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 150494 ave 251670 max 54664 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 601974
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Ave neighs/atom = 150.494
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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) = 4.136 | 4.393 | 4.673 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137
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1550 0.55327047 -6.2750129 0 -5.4453147 -1.9506601 4738.2137
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1600 0.54419056 -6.2612631 0 -5.4451813 -1.8559469 4738.2137
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1650 0.54710007 -6.2661977 0 -5.4457528 -1.8882828 4738.2137
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1700 0.53665429 -6.250492 0 -5.4457118 -1.8067907 4738.2137
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1750 0.54864943 -6.2681198 0 -5.4453514 -1.8662924 4738.2137
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1800 0.54477002 -6.2615118 0 -5.4445611 -1.835304 4738.2137
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1850 0.54143129 -6.2555621 0 -5.4436182 -1.8005839 4738.2137
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1900 0.53994573 -6.254175 0 -5.4444588 -1.7770422 4738.2137
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1950 0.54665379 -6.2640981 0 -5.4443224 -1.7946205 4738.2137
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2000 0.54548501 -6.2623919 0 -5.4443689 -1.8063177 4738.2137
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Loop time of 3.48709 on 4 procs for 500 steps with 4000 atoms
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Performance: 61942.848 tau/day, 143.386 timesteps/s
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96.7% 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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---------------------------------------------------------------
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Pair | 0.42099 | 1.3571 | 2.3564 | 80.4 | 38.92
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Neigh | 0.083965 | 0.4942 | 0.96204 | 58.6 | 14.17
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Comm | 0.25895 | 1.6131 | 2.9631 | 106.2 | 46.26
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Output | 0.00042915 | 0.00068706 | 0.0012567 | 0.0 | 0.02
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Modify | 0.0051193 | 0.010964 | 0.017898 | 5.5 | 0.31
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Other | | 0.01109 | | | 0.32
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Nlocal: 1000 ave 2036 max 127 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 8722.75 ave 10448 max 7456 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 151642 ave 269558 max 35372 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 606566
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Ave neighs/atom = 151.642
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Neighbor list builds = 56
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Dangerous builds = 0
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Total wall time: 0:00:12
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