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lammps/bench-nsf/wat/log.wat-cpu-2m1t-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 4 by 4 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 4 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 = 2744 900 1764
Memory usage per processor = 11.1212 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 6.741379
20 -1.1179164 300 0.80326904 10.22405 1000000 29606.506 4.8259055
30 -1.5670225 300 0.48379426 10.089733 1000000 -12190.612 3.4491049
40 -1.9198995 300 0.31756189 9.8649171 1000000 -52802.269 3.5156712
50 -2.2736063 300 0.26723838 9.6089211 1000000 -25090.714 3.5000805
60 -2.4288467 300 0.25676863 9.4795354 1000000 3346.1223 3.5161707
61 -2.4290829 300 0.25666245 9.4792524 1000000 5057.583 1.5326003
Loop time of 15.6529 on 64 procs for 61 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.39940196 -2.42884666708 -2.42908290427
Force two-norm initial, final = 2.24428e+07 2294.6
Force max component initial, final = 305690 24.2716
Final line search alpha, max atom move = 1.45951e-05 0.000354246
Iterations, force evaluations = 61 262
Pair time (%) = 13.0045 (83.081)
Bond time (%) = 0.042261 (0.269989)
Kspce time (%) = 2.03122 (12.9766)
Neigh time (%) = 0 (0)
Comm time (%) = 0.481729 (3.07758)
Outpt time (%) = 0.00219841 (0.0140448)
Other time (%) = 0.0909053 (0.580759)
FFT time (% of Kspce) = 0.1422 (7.00073)
FFT Gflps 3d (1d only) = 4.30327 81.2365
Nlocal: 1312.5 ave 1369 max 1259 min
Histogram: 8 0 16 0 0 16 8 8 0 8
Nghost: 15043 ave 15311 max 14729 min
Histogram: 8 0 8 8 0 8 16 8 0 8
Neighs: 1.03562e+06 ave 1.08657e+06 max 986357 min
Histogram: 8 0 16 0 0 16 16 0 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 = 2744 900 1764
SHAKE stats (type/ave/delta) on step 0
1 0.957306 0.000610672
1 104.486 0.058182
Memory usage per processor = 10.794 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.430529 450.00268 0.25666245 9.4792524 1000000 2614.6351 0
500 -3.1082306 305.19203 0.31235643 8.751614 955851.57 -1339.7211 17.835209
1000 -3.2026595 298.55767 0.33530394 8.6345315 906341.41 -964.25059 15.832953
1500 -3.2369494 299.1401 0.34130859 8.5945644 871954.34 -588.08832 15.486769
SHAKE stats (type/ave/delta) on step 2000
1 0.957189 5.78787e-06
1 104.52 0.000609594
2000 -3.2468663 299.22089 0.34384811 8.5821492 849967.93 -216.07321 14.818792
2500 -3.2610628 297.38339 0.34793505 8.5638145 837238.92 -1.3174329 15.006685
3000 -3.2641755 299.84838 0.34210358 8.5666361 831166.31 -43.13779 14.406267
3500 -3.2650817 300.53039 0.34046741 8.5672154 831823.93 -107.92425 14.371323
SHAKE stats (type/ave/delta) on step 4000
1 0.9572 3.9622e-06
1 104.52 0.000478372
4000 -3.2621899 300.19169 0.34646222 8.564328 830223.87 118.36717 14.271857
4500 -3.2674978 299.95775 0.3512994 8.5540447 828919.48 205.81749 14.643973
5000 -3.2685455 298.88669 0.34657923 8.5577233 827767.77 109.4827 14.012518
5500 -3.2617197 299.98788 0.34173663 8.5694521 830258.04 -19.668296 14.53831
SHAKE stats (type/ave/delta) on step 6000
1 0.957198 4.59066e-06
1 104.52 0.00062038
6000 -3.2688665 300.85107 0.34289059 8.5610444 828925.49 -16.1408 14.272421
6500 -3.267101 301.21832 0.3458645 8.5599014 830755.76 37.116843 14.790427
7000 -3.2683017 299.78946 0.34266891 8.5618897 828396.61 -12.276035 14.221958
7500 -3.2667969 298.1766 0.34181139 8.5642929 828416.27 -2.5017675 14.53295
SHAKE stats (type/ave/delta) on step 8000
1 0.957202 4.57153e-06
1 104.52 0.000436105
8000 -3.2665271 298.53619 0.34627554 8.5600826 829244.16 58.956775 13.314039
8500 -3.2654719 300.88703 0.34544955 8.5619147 831759.78 19.720232 14.710121
9000 -3.2671269 300.93565 0.34223462 8.5635459 829635.49 -22.312087 14.310937
9500 -3.2688326 298.54266 0.34007719 8.5638633 830232.88 -112.08515 14.18464
SHAKE stats (type/ave/delta) on step 10000
1 0.957202 4.04686e-06
1 104.52 0.000488093
10000 -3.2653117 301.07648 0.34653149 8.5608529 830692.68 82.196676 14.291657
Loop time of 682.827 on 64 procs for 10000 steps with 84000 atoms
Pair time (%) = 483.517 (70.8109)
Bond time (%) = 0.0232459 (0.00340436)
Kspce time (%) = 85.0083 (12.4495)
Neigh time (%) = 57.1715 (8.37276)
Comm time (%) = 24.0325 (3.51955)
Outpt time (%) = 0.00800043 (0.00117166)
Other time (%) = 33.0673 (4.8427)
FFT time (% of Kspce) = 23.1795 (27.2673)
FFT Gflps 3d (1d only) = 4.32778 79.4241
Nlocal: 1312.5 ave 1342 max 1258 min
Histogram: 1 1 2 1 9 14 7 13 11 5
Nghost: 16946.1 ave 17036 max 16791 min
Histogram: 1 2 0 5 9 13 8 9 8 9
Neighs: 1.24822e+06 ave 1.31698e+06 max 1.16345e+06 min
Histogram: 3 1 5 9 10 7 9 11 4 5
Total # of neighbors = 79886025
Ave neighs/atom = 951.024
Ave special neighs/atom = 2
Neighbor list builds = 888
Dangerous builds = 0
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