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lammps/bench-nsf/wat/log.wat-cpu-6m1t-kraken
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LAMMPS (19 Nov 2010-ICMS)
# TIPS water from charmm.
boundary p p p
units real
atom_style full
special_bonds lj/coul 0.0 0.0 1.0
read_data data.wat
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (-5.2675 -4.985 -4.9345) to (4.7325 5.015 5.0655)
4 by 6 by 8 processor grid
84 atoms
56 bonds
28 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
replicate ${num} ${num} ${num}
replicate 10 ${num} ${num}
replicate 10 10 ${num}
replicate 10 10 10
orthogonal box = (-5.2675 -4.985 -4.9345) to (94.7325 95.015 95.0655)
4 by 6 by 8 processor grid
84000 atoms
56000 bonds
28000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long 14.0
pair_modify mix arithmetic
pair_coeff 2 2 0.1521000000 3.15057
pair_coeff 1 1 0.046 0.400014
# 100x larger for minimize
angle_style harmonic
angle_coeff 1 5500 104.52
# 100x larger constant for minimize
bond_style harmonic
bond_coeff 1 45000 0.9572
kspace_style pppm 1.0e-4
velocity all create 300 234324 dist gaussian
neighbor 2.5 bin
neigh_modify delay 2 every 1 check yes
thermo 10
thermo_style custom step pe temp evdwl ecoul vol press spcpu
thermo_modify norm yes
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Resetting reneighboring criteria during minimization
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 1540 324 1848
Memory usage per processor = 7.75662 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 656.3994 300 623.49127 10.7913 1000000 13052196 0
10 2.1079218 300 3.7701061 10.339662 1000000 159414.93 10.707797
20 -1.1179164 300 0.80326907 10.22405 1000000 29606.435 7.3382479
30 -1.5413127 300 0.45440054 10.075508 1000000 -5658.5437 5.1318499
40 -1.8832432 300 0.34633205 9.9162614 1000000 28033.599 4.3411616
50 -2.1596493 300 0.28190957 9.7064488 1000000 6042.3853 4.876745
60 -2.2885822 300 0.26657623 9.5969339 1000000 18386.744 4.1734729
65 -2.332473 300 0.26307523 9.5673715 1000000 4893.0497 3.5575948
Loop time of 12.4012 on 192 procs for 65 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401958 -2.33229468198 -2.33247303293
Force two-norm initial, final = 2.24428e+07 1730.52
Force max component initial, final = 305690 21.2948
Final line search alpha, max atom move = 5.00893e-06 0.000106664
Iterations, force evaluations = 65 313
Pair time (%) = 5.53064 (44.5977)
Bond time (%) = 0.0170702 (0.13765)
Kspce time (%) = 5.84682 (47.1473)
Neigh time (%) = 0 (0)
Comm time (%) = 0.865903 (6.98244)
Outpt time (%) = 0.00226127 (0.0182343)
Other time (%) = 0.138474 (1.11662)
FFT time (% of Kspce) = 0.845668 (14.4637)
FFT Gflps 3d (1d only) = 0.771049 198.232
Nlocal: 437.5 ave 487 max 387 min
Histogram: 8 16 8 32 16 48 16 32 8 8
Nghost: 10499.7 ave 10873 max 10263 min
Histogram: 8 40 48 16 16 16 16 16 8 8
Neighs: 345208 ave 411558 max 294959 min
Histogram: 16 16 24 32 32 24 16 24 0 8
Total # of neighbors = 66280000
Ave neighs/atom = 789.048
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
thermo 500
fix 1 all shake 0.0001 20 2000 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
28000 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
timestep 2.0
run 10000
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 1540 324 1848
SHAKE stats (type/ave/delta) on step 0
1 0.957311 0.000373645
1 104.485 0.108094
Memory usage per processor = 7.4441 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3339536 450.00268 0.26307523 9.5673715 1000000 3415.7941 0
500 -3.0965437 306.89185 0.31144539 8.7639763 959499.98 -1305.1232 25.630454
1000 -3.2019513 299.28489 0.33803663 8.6324646 909881.25 -918.99691 24.589112
1500 -3.2315125 297.78482 0.34180482 8.5993473 875103.19 -578.53795 24.26369
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 5.14594e-06
1 104.52 0.000440008
2000 -3.2456498 300.36289 0.3442019 8.5828853 852504.1 -235.64853 23.625835
2500 -3.2603291 301.37552 0.34305886 8.5693961 838816.66 -130.70507 23.291917
3000 -3.2675439 300.78014 0.34644061 8.5587943 831272.03 36.70687 23.061098
3500 -3.267466 299.2436 0.34316658 8.5622896 828845.48 2.4426423 22.877272
SHAKE stats (type/ave/delta) on step 4000
1 0.957201 4.04177e-06
1 104.52 0.000450165
4000 -3.2705333 299.10224 0.34219339 8.5602044 829525 -68.526293 22.671
4500 -3.2664854 300.9659 0.34488432 8.5614209 826217.8 136.9385 23.184648
5000 -3.2657184 300.10526 0.34427724 8.5627759 829790.76 1.4076215 22.215397
5500 -3.2687694 299.54022 0.34251545 8.5616194 828079.84 -7.3904078 23.064579
SHAKE stats (type/ave/delta) on step 6000
1 0.957199 4.15823e-06
1 104.52 0.000587369
6000 -3.2693663 298.25407 0.34219766 8.5613077 830752.21 -87.456588 22.6827
6500 -3.263847 299.68818 0.34258405 8.5663426 826601.21 70.686947 22.317941
7000 -3.2647311 300.43542 0.34273155 8.5654377 829943.31 5.3523823 23.055551
7500 -3.2664504 298.08507 0.34160188 8.5648135 829441.3 -39.963157 23.326366
SHAKE stats (type/ave/delta) on step 8000
1 0.957198 4.17898e-06
1 104.52 0.000492297
8000 -3.2585013 300.92969 0.3383492 8.5759686 830595.95 -54.270799 23.175749
8500 -3.2648639 299.14215 0.345095 8.5629333 827541.55 96.622647 22.800435
9000 -3.267811 300.60054 0.34054102 8.5647458 827827.4 -33.461682 22.963775
9500 -3.2628668 300.97999 0.34151803 8.5685138 829552.94 10.407906 23.099483
SHAKE stats (type/ave/delta) on step 10000
1 0.957201 4.28515e-06
1 104.52 0.000437212
10000 -3.2588617 300.30595 0.33664437 8.5773697 831708.21 -149.87244 22.955751
Loop time of 430.694 on 192 procs for 10000 steps with 84000 atoms
Pair time (%) = 167.416 (38.8712)
Bond time (%) = 0.0252663 (0.00586641)
Kspce time (%) = 179.486 (41.6736)
Neigh time (%) = 18.7471 (4.35275)
Comm time (%) = 35.0826 (8.14558)
Outpt time (%) = 0.00815926 (0.00189444)
Other time (%) = 29.9295 (6.94912)
FFT time (% of Kspce) = 129.636 (72.2266)
FFT Gflps 3d (1d only) = 0.773823 200.502
Nlocal: 437.5 ave 469 max 405 min
Histogram: 3 9 18 26 34 34 38 20 6 4
Nghost: 11997.2 ave 12176 max 11850 min
Histogram: 4 12 20 33 51 38 21 11 0 2
Neighs: 415546 ave 474125 max 364487 min
Histogram: 5 10 24 34 37 36 26 15 3 2
Total # of neighbors = 79784797
Ave neighs/atom = 949.819
Ave special neighs/atom = 2
Neighbor list builds = 889
Dangerous builds = 0
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