228 lines
10 KiB
Groff
228 lines
10 KiB
Groff
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 = 0.000421762 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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fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 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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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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Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 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 2.69458 on 4 procs for 500 steps with 4000 atoms
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Performance: 80160.913 tau/day, 185.558 timesteps/s
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94.2% 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 | 1.0903 | 1.4509 | 1.7199 | 22.5 | 53.84
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Neigh | 0.31688 | 0.47906 | 0.71852 | 24.2 | 17.78
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Comm | 0.60463 | 0.72402 | 0.84257 | 12.7 | 26.87
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Output | 0.00035119 | 0.00067121 | 0.0015202 | 0.0 | 0.02
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Modify | 0.00811 | 0.010936 | 0.014029 | 2.7 | 0.41
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Other | | 0.02904 | | | 1.08
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Nlocal: 1000 ave 1504 max 634 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8759.25 ave 9896 max 8021 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 149308 ave 179946 max 116419 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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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) = 4.097 | 4.288 | 4.475 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 2.64502 on 4 procs for 500 steps with 4000 atoms
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Performance: 81662.873 tau/day, 189.034 timesteps/s
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93.3% 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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Pair | 1.1279 | 1.4127 | 1.6268 | 18.0 | 53.41
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Neigh | 0.32225 | 0.49572 | 0.76053 | 26.2 | 18.74
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Comm | 0.64504 | 0.6974 | 0.75498 | 5.7 | 26.37
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Output | 0.00035477 | 0.00062996 | 0.001343 | 0.0 | 0.02
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Modify | 0.0077929 | 0.010538 | 0.013856 | 2.6 | 0.40
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Other | | 0.02803 | | | 1.06
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Nlocal: 1000 ave 1437 max 597 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Nghost: 8674 ave 9370 max 8013 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 150170 ave 187030 max 102149 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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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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fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
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run 500
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Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 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 -1.9170271 4738.2137
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1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
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1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
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1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
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1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
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Loop time of 2.61342 on 4 procs for 500 steps with 4000 atoms
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Performance: 82650.254 tau/day, 191.320 timesteps/s
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93.1% 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 | 1.222 | 1.4442 | 1.5812 | 12.3 | 55.26
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Neigh | 0.29672 | 0.48201 | 0.73859 | 27.6 | 18.44
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Comm | 0.59138 | 0.65738 | 0.70906 | 6.5 | 25.15
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Output | 0.00036502 | 0.00091559 | 0.0020845 | 0.0 | 0.04
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Modify | 0.0095406 | 0.012674 | 0.017643 | 2.8 | 0.48
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Other | | 0.01621 | | | 0.62
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Nlocal: 1000 ave 1446 max 670 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8641 ave 9376 max 8019 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Neighs: 150494 ave 184085 max 105390 min
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Histogram: 1 0 1 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) = 4.08 | 4.269 | 4.458 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
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1550 0.55327018 -6.2750125 0 -5.4453148 -1.9506585 4738.2137
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1600 0.5441901 -6.2612622 0 -5.4451811 -1.8559436 4738.2137
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1650 0.54710046 -6.2661938 0 -5.4457483 -1.8882766 4738.2137
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1700 0.5366569 -6.2504957 0 -5.4457116 -1.8067998 4738.2137
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1750 0.5486468 -6.2681121 0 -5.4453476 -1.8662631 4738.2137
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1800 0.54476176 -6.2615037 0 -5.4445653 -1.8352743 4738.2137
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1850 0.5414305 -6.2555519 0 -5.4436091 -1.8005747 4738.2137
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1900 0.53992655 -6.2541344 0 -5.444447 -1.7768718 4738.2137
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1950 0.54666071 -6.2640943 0 -5.4443082 -1.7947052 4738.2137
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2000 0.54556196 -6.2625262 0 -5.4443879 -1.8071631 4738.2137
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Loop time of 2.81593 on 4 procs for 500 steps with 4000 atoms
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Performance: 76706.532 tau/day, 177.561 timesteps/s
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90.7% 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 | 1.2508 | 1.4839 | 1.6521 | 13.4 | 52.70
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Neigh | 0.34188 | 0.54016 | 0.82358 | 27.6 | 19.18
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Comm | 0.70575 | 0.75254 | 0.80167 | 4.6 | 26.72
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Output | 0.00041604 | 0.001362 | 0.0041099 | 4.3 | 0.05
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Modify | 0.010564 | 0.013653 | 0.018 | 2.7 | 0.48
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Other | | 0.02432 | | | 0.86
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Nlocal: 1000 ave 1555 max 569 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 8672.75 ave 9821 max 7993 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Neighs: 151656 ave 164603 max 133455 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 606625
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Ave neighs/atom = 151.656
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Neighbor list builds = 56
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Dangerous builds = 0
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Total wall time: 0:00:10
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