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lammps/bench-nsf/wat/log.wat-cpu-3m1t-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 6 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 6 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 = 2156 540 1764
Memory usage per processor = 9.39707 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 159414.92 9.2625356
20 -1.1179165 300 0.80326921 10.22405 1000000 29606.126 6.3558323
30 -1.5741509 300 0.45296386 10.074196 1000000 -26785.314 4.6450206
40 -1.7861157 300 0.36412739 10.001077 1000000 9067.3808 3.7184509
50 -1.9758386 300 0.31148316 9.8638038 1000000 -1163.9643 3.7068119
60 -2.1715891 300 0.27917593 9.6926709 1000000 -4890.6211 3.8556255
70 -2.3731854 300 0.25352965 9.4904853 1000000 -42363.852 4.3852414
75 -2.419166 300 0.25283868 9.492901 1000000 4946.313 2.5385672
Loop time of 17.0365 on 96 procs for 75 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.41893323297 -2.4191660118
Force two-norm initial, final = 2.24428e+07 1776.45
Force max component initial, final = 305690 18.7076
Final line search alpha, max atom move = 1.66271e-05 0.000311053
Iterations, force evaluations = 75 379
Pair time (%) = 12.6017 (73.9686)
Bond time (%) = 0.042644 (0.250309)
Kspce time (%) = 3.49802 (20.5325)
Neigh time (%) = 0 (0)
Comm time (%) = 0.766705 (4.50036)
Outpt time (%) = 0.00294927 (0.0173114)
Other time (%) = 0.124529 (0.730951)
FFT time (% of Kspce) = 0.3712 (10.6117)
FFT Gflps 3d (1d only) = 2.02685 123.723
Nlocal: 875 ave 916 max 841 min
Histogram: 8 16 8 16 0 24 0 8 0 16
Nghost: 13101.3 ave 13284 max 12893 min
Histogram: 8 16 0 8 8 16 0 24 0 16
Neighs: 690417 ave 728833 max 660280 min
Histogram: 16 0 24 8 8 16 0 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 = 2156 540 1764
SHAKE stats (type/ave/delta) on step 0
1 0.957307 0.0003579
1 104.488 0.051677
Memory usage per processor = 9.07722 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.4203949 450.00268 0.25283868 9.492901 1000000 2629.4675 0
500 -3.1121236 306.8712 0.31699805 8.7430382 956015.15 -1259.0958 22.777106
1000 -3.2022665 300.47383 0.33714873 8.6330653 906345.66 -892.01659 20.20825
1500 -3.2356127 300.48508 0.34664571 8.5902983 873342.34 -473.45752 20.392983
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.31944e-06
1 104.52 0.000512724
2000 -3.251077 299.87416 0.34113095 8.5804813 850906.79 -347.93767 19.133298
2500 -3.2634251 300.59175 0.34157335 8.5677424 838789.57 -183.58618 19.581354
3000 -3.2663039 301.02526 0.34202533 8.5644364 831186.37 -59.504064 18.09779
3500 -3.2671167 299.73891 0.34169846 8.5639424 830128.92 -52.122208 18.370001
SHAKE stats (type/ave/delta) on step 4000
1 0.9572 4.31921e-06
1 104.52 0.000504274
4000 -3.2673292 298.12483 0.34629875 8.5592309 826480.33 124.71167 18.845262
4500 -3.2666311 301.7959 0.34393853 8.5622037 828529.99 56.028973 19.30037
5000 -3.2669712 298.48816 0.34530276 8.5606289 830628.53 10.714514 18.856587
5500 -3.263195 299.65469 0.34066258 8.5689904 828790.6 -16.337882 19.046924
SHAKE stats (type/ave/delta) on step 6000
1 0.957198 3.98128e-06
1 104.52 0.000434356
6000 -3.2709123 301.21264 0.34715121 8.5547811 828999.65 90.728023 18.364801
6500 -3.2713888 299.40417 0.34003012 8.5614064 828283.1 -94.988644 18.728478
7000 -3.2670064 300.10158 0.34415385 8.5616226 828743.19 20.448906 18.812139
7500 -3.2645843 299.51143 0.33987574 8.5684161 829630.29 -94.821978 19.101366
SHAKE stats (type/ave/delta) on step 8000
1 0.957204 4.45667e-06
1 104.52 0.00047345
8000 -3.265482 300.15724 0.33899671 8.5684898 829511.99 -104.00922 18.66062
8500 -3.262708 300.2002 0.34195317 8.5681783 831738.83 -44.129939 19.074621
9000 -3.2674889 301.84408 0.34203136 8.5633886 829333.9 -19.395093 18.797631
9500 -3.2621199 299.727 0.34163541 8.5691622 829441.72 -10.211256 19.00746
SHAKE stats (type/ave/delta) on step 10000
1 0.957198 4.38459e-06
1 104.52 0.000503582
10000 -3.2685663 299.33256 0.3413353 8.56284 828655.67 -64.022849 18.607185
Loop time of 522.392 on 96 procs for 10000 steps with 84000 atoms
Pair time (%) = 329.39 (63.0543)
Bond time (%) = 0.0235752 (0.00451293)
Kspce time (%) = 100.961 (19.3267)
Neigh time (%) = 38.0149 (7.27708)
Comm time (%) = 25.3768 (4.85781)
Outpt time (%) = 0.00758399 (0.00145178)
Other time (%) = 28.6173 (5.47812)
FFT time (% of Kspce) = 49.3884 (48.9182)
FFT Gflps 3d (1d only) = 2.03116 127.039
Nlocal: 875 ave 915 max 844 min
Histogram: 5 9 17 17 15 6 13 8 3 3
Nghost: 14863.3 ave 14958 max 14742 min
Histogram: 3 6 0 8 16 23 17 10 6 7
Neighs: 834058 ave 885552 max 786217 min
Histogram: 6 7 16 8 14 14 9 6 8 8
Total # of neighbors = 80069565
Ave neighs/atom = 953.209
Ave special neighs/atom = 2
Neighbor list builds = 889
Dangerous builds = 0
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