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lammps/bench-nsf/wat/log.wat-cpu-1m1t-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)
2 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)
2 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 = 4508 2592 2898
Memory usage per processor = 18.4486 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 3.2562705
20 -1.1179165 300 0.80326914 10.22405 1000000 29606.271 2.4616215
30 -1.5639616 300 0.45384943 10.075243 1000000 -13186.249 1.7665619
40 -1.7036418 300 0.41802635 10.031894 1000000 18811.447 1.2123159
50 -1.8532827 300 0.36451342 9.9378512 1000000 5851.5737 0.92469745
60 -2.0819128 300 0.30149714 9.7693067 1000000 31496.027 1.631207
70 -2.2727687 300 0.26052422 9.6283332 1000000 3763.1145 1.5738237
80 -2.3864783 300 0.25156979 9.5259451 1000000 3077.8392 1.0753529
89 -2.5429192 300 0.23688674 9.3872395 1000000 3261.82 1.126814
Loop time of 61.6279 on 32 procs for 89 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.54276678205 -2.5429191789
Force two-norm initial, final = 2.24428e+07 939.714
Force max component initial, final = 305690 6.36809
Final line search alpha, max atom move = 5.21782e-06 3.32275e-05
Iterations, force evaluations = 89 461
Pair time (%) = 45.6157 (74.0179)
Bond time (%) = 0.14565 (0.236337)
Kspce time (%) = 10.4379 (16.9369)
Neigh time (%) = 0 (0)
Comm time (%) = 4.71965 (7.6583)
Outpt time (%) = 0.0124789 (0.0202487)
Other time (%) = 0.69659 (1.13032)
FFT time (% of Kspce) = 0.200367 (1.91962)
FFT Gflps 3d (1d only) = 4.45587 38.9725
Nlocal: 2625 ave 2655 max 2595 min
Histogram: 8 8 0 0 0 0 0 0 8 8
Nghost: 21035.8 ave 21338 max 20699 min
Histogram: 8 0 0 0 0 16 0 0 0 8
Neighs: 2.07125e+06 ave 2.10053e+06 max 2.0368e+06 min
Histogram: 8 0 8 0 0 0 0 0 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 = 4508 2592 2898
SHAKE stats (type/ave/delta) on step 0
1 0.957316 0.000327856
1 104.486 0.0474217
Memory usage per processor = 17.9467 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.544211 450.00268 0.23688674 9.3872395 1000000 1439.5403 0
500 -3.1263044 303.66357 0.32087335 8.7249538 948571.08 -1185.8268 9.4200968
1000 -3.2076385 298.77163 0.34020306 8.6246333 900740.24 -776.51881 7.3492282
1500 -3.2344491 301.08122 0.3377106 8.6005323 868607.38 -571.21657 8.0593291
SHAKE stats (type/ave/delta) on step 2000
1 0.957189 4.04444e-06
1 104.52 0.000431215
2000 -3.2549425 300.2453 0.34435889 8.5734756 847157.73 -215.91062 7.1136124
2500 -3.2598453 300.45094 0.34410997 8.5689179 835494.29 -17.562267 7.2839275
3000 -3.2688835 299.94974 0.34311166 8.5608872 831059.31 -51.682115 7.3451218
3500 -3.2674682 298.97372 0.34320328 8.562033 831462.98 -80.439369 7.0289194
SHAKE stats (type/ave/delta) on step 4000
1 0.9572 3.90722e-06
1 104.52 0.000462294
4000 -3.2666518 300.28189 0.34306007 8.5630326 830683.6 -31.823452 7.0160324
4500 -3.2668065 298.85316 0.34489927 8.5611292 828449.54 67.664616 7.5306591
5000 -3.2647032 300.84527 0.34128704 8.5667825 830241.93 -36.487977 6.7215664
5500 -3.2669463 300.65691 0.34112632 8.5647255 830611.05 -72.119383 7.3251697
SHAKE stats (type/ave/delta) on step 6000
1 0.957201 4.43809e-06
1 104.52 0.000607547
6000 -3.2634546 298.69088 0.33930185 8.5701278 831158.32 -122.73979 7.1720483
6500 -3.2660358 298.46679 0.34952306 8.5571729 830216.64 114.58757 6.9275077
7000 -3.2660377 300.83563 0.34595501 8.560865 829584.57 85.806064 6.5715208
7500 -3.2671322 300.97249 0.34677834 8.5587841 829214.18 81.888535 7.3286752
SHAKE stats (type/ave/delta) on step 8000
1 0.9572 4.37486e-06
1 104.52 0.000521558
8000 -3.2686776 301.21776 0.34785252 8.5562949 830584.5 83.812337 7.2789053
8500 -3.2625534 299.52198 0.34378317 8.5663862 829211.66 58.515758 7.1867834
9000 -3.2640095 300.78863 0.33698957 8.5718426 831177.71 -190.88649 6.9287929
9500 -3.2667458 299.07834 0.34171486 8.5643986 827691.4 -7.2567046 7.1213476
SHAKE stats (type/ave/delta) on step 10000
1 0.957204 4.21924e-06
1 104.52 0.000503324
10000 -3.2701919 300.33266 0.34427943 8.5585351 828925.45 -8.2624565 6.7122565
Loop time of 1382.93 on 32 procs for 10000 steps with 84000 atoms
Pair time (%) = 965.589 (69.8221)
Bond time (%) = 0.0230094 (0.00166382)
Kspce time (%) = 162.512 (11.7513)
Neigh time (%) = 117.23 (8.47692)
Comm time (%) = 54.4906 (3.94024)
Outpt time (%) = 0.00838654 (0.000606434)
Other time (%) = 83.0747 (6.00716)
FFT time (% of Kspce) = 22.5053 (13.8484)
FFT Gflps 3d (1d only) = 4.45741 38.991
Nlocal: 2625 ave 2669 max 2574 min
Histogram: 2 0 3 5 5 3 3 7 0 4
Nghost: 23222.9 ave 23338 max 23118 min
Histogram: 2 1 4 7 2 7 2 4 1 2
Neighs: 2.50167e+06 ave 2.63893e+06 max 2.38155e+06 min
Histogram: 1 5 4 3 4 5 4 3 2 1
Total # of neighbors = 80053284
Ave neighs/atom = 953.015
Ave special neighs/atom = 2
Neighbor list builds = 892
Dangerous builds = 0
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