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lammps/bench-nsf/wat/log.wat-cpu-lincoln
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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 4 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 4 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 = 1960 540 2352
Memory usage per processor = 8.72471 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 656.3994 300 623.49127 10.7913 1000000 13052196 0
10 2.1079217 300 3.7701061 10.339662 1000000 159414.93 6.5440528
20 -1.1179163 300 0.80326894 10.22405 1000000 29606.737 4.520812
30 -1.565637 300 0.48498955 10.09106 1000000 -9720.7263 3.2588501
40 -1.7521723 300 0.38337442 10.011575 1000000 -9717.296 2.936718
50 -2.041921 300 0.2980556 9.8047651 1000000 4445.0762 3.3128707
60 -2.1217723 300 0.28467086 9.7530653 1000000 11260.132 2.3819851
70 -2.3039635 300 0.26580568 9.5925948 1000000 6114.5889 2.9046682
71 -2.304136 300 0.26579788 9.5920309 1000000 4743.0896 1.5997364
Loop time of 21.4991 on 128 procs for 71 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.30396353471 -2.30413602892
Force two-norm initial, final = 2.24428e+07 2144.75
Force max component initial, final = 305690 30.6394
Final line search alpha, max atom move = 1.15197e-05 0.000352957
Iterations, force evaluations = 71 341
Pair time (%) = 10.9172 (50.7799)
Bond time (%) = 0.0307343 (0.142956)
Kspce time (%) = 7.95948 (37.0224)
Neigh time (%) = 0 (0)
Comm time (%) = 1.81289 (8.43241)
Outpt time (%) = 0.0268552 (0.124913)
Other time (%) = 0.751913 (3.49742)
FFT time (% of Kspce) = 1.12481 (14.1317)
FFT Gflps 3d (1d only) = 0.633209 78.458
Nlocal: 656.25 ave 699 max 608 min
Histogram: 8 0 16 0 40 24 16 8 8 8
Nghost: 12144.8 ave 12548 max 11847 min
Histogram: 8 24 16 16 24 16 0 8 8 8
Neighs: 517812 ave 586277 max 471216 min
Histogram: 16 24 24 8 8 0 24 8 8 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 = 1960 540 2352
SHAKE stats (type/ave/delta) on step 0
1 0.957313 0.000404366
1 104.482 0.133805
Memory usage per processor = 8.40853 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3059177 450.00268 0.26579788 9.5920309 1000000 3658.957 0
500 -3.0929158 306.79173 0.30911976 8.7700276 960754.84 -1382.6662 15.587445
1000 -3.2035167 299.35916 0.33849549 8.6304674 909770.63 -938.80833 14.964028
1500 -3.2293099 299.55997 0.3444371 8.598827 875458.41 -510.36891 14.618629
SHAKE stats (type/ave/delta) on step 2000
1 0.957189 5.41396e-06
1 104.52 0.000487686
2000 -3.2488078 299.02385 0.34653266 8.5775743 852505.86 -227.16319 14.358206
2500 -3.2614889 299.47273 0.34393715 8.5674115 837920.91 -101.6644 14.126043
3000 -3.2665911 298.91565 0.34880016 8.5574682 832254.27 70.045519 14.069354
3500 -3.266317 300.53199 0.34299649 8.5635842 830651.03 -21.707672 14.147169
SHAKE stats (type/ave/delta) on step 4000
1 0.957201 5.72248e-06
1 104.52 0.000531402
4000 -3.2648638 300.24974 0.34553469 8.5624615 828625.17 105.33024 14.009737
4500 -3.2657856 299.15731 0.34510805 8.5618976 829967.4 62.688142 14.096111
5000 -3.2641379 298.72728 0.34136881 8.5671979 829948.85 -34.465021 14.099847
5500 -3.2659775 300.49188 0.34223652 8.5646223 827430.03 43.890762 14.08208
SHAKE stats (type/ave/delta) on step 6000
1 0.957203 5.1142e-06
1 104.52 0.000540326
6000 -3.2699746 301.21748 0.34492413 8.5579948 828572.57 29.56964 14.047389
6500 -3.2647785 300.63885 0.3445632 8.5634696 830115.82 34.135163 14.146597
7000 -3.267256 300.05846 0.3407242 8.5649851 829653.87 -61.592163 13.406575
7500 -3.2646979 299.2853 0.34276328 8.565249 828067.07 27.710164 13.941739
SHAKE stats (type/ave/delta) on step 8000
1 0.957198 4.25818e-06
1 104.52 0.000514121
8000 -3.269236 299.37446 0.34703463 8.5565625 829041.41 73.949492 14.068431
8500 -3.2608417 302.08168 0.33939093 8.5724235 830140.59 -50.850306 14.027124
9000 -3.265775 299.01624 0.34688509 8.560254 831449.03 38.236599 14.076004
9500 -3.266585 302.37621 0.34334606 8.5629022 830289.37 -13.190583 13.898698
SHAKE stats (type/ave/delta) on step 10000
1 0.957202 5.06436e-06
1 104.52 0.000482308
10000 -3.2649448 299.37986 0.34390651 8.5640057 828402.08 52.13532 13.884565
Loop time of 705.711 on 128 procs for 10000 steps with 84000 atoms
Pair time (%) = 311.542 (44.1459)
Bond time (%) = 0.029292 (0.00415071)
Kspce time (%) = 229.667 (32.544)
Neigh time (%) = 30.851 (4.37161)
Comm time (%) = 62.1643 (8.80875)
Outpt time (%) = 0.0781048 (0.0110675)
Other time (%) = 71.3795 (10.1145)
FFT time (% of Kspce) = 155.4 (67.6634)
FFT Gflps 3d (1d only) = 0.64553 77.7622
Nlocal: 656.25 ave 703 max 611 min
Histogram: 1 6 13 23 21 21 28 11 3 1
Nghost: 13816.4 ave 13948 max 13655 min
Histogram: 2 3 10 15 17 26 28 15 9 3
Neighs: 625845 ave 705060 max 562391 min
Histogram: 4 9 26 20 21 17 13 9 7 2
Total # of neighbors = 80108202
Ave neighs/atom = 953.669
Ave special neighs/atom = 2
Neighbor list builds = 893
Dangerous builds = 0
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