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lammps/bench-nsf/wat/log.wat-omp-2m3t-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
using 3 OpenMP thread(s) per MPI task
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
using 3 OpenMP thread(s) per MPI task
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/omp 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 = 11.1223 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 5.0914136
20 -1.1179164 300 0.80326904 10.22405 1000000 29606.506 3.4566948
30 -1.5670224 300 0.48379422 10.089733 1000000 -12190.709 2.4987525
40 -1.9196665 300 0.31756901 9.864924 1000000 -52996.713 2.5485706
50 -2.2638532 300 0.26748691 9.6256909 1000000 -10911.349 2.4947337
60 -2.3446417 300 0.25956919 9.5589932 1000000 2828.6117 1.9698041
70 -2.4255636 300 0.2491072 9.4900761 1000000 3718.0364 1.6769696
80 -2.5876053 300 0.22900132 9.350634 1000000 12925.421 2.1219575
82 -2.5888936 300 0.22908091 9.3496822 1000000 2062.2966 1.157674
Loop time of 34.2716 on 192 procs (64 MPI x 3 OpenMP) for 82 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.58878232786 -2.58889361236
Force two-norm initial, final = 2.24428e+07 996.142
Force max component initial, final = 305690 6.52707
Final line search alpha, max atom move = 7.85151e-06 5.12473e-05
Iterations, force evaluations = 82 417
Pair time (%) = 24.5209 (71.5489)
Bond time (%) = 0.0651888 (0.190212)
Kspce time (%) = 8.716 (25.4322)
Neigh time (%) = 0 (0)
Comm time (%) = 0.795537 (2.32127)
Outpt time (%) = 0.00303968 (0.00886939)
Other time (%) = 0.170888 (0.498629)
FFT time (% of Kspce) = 0.200509 (2.30047)
FFT Gflps 3d (1d only) = 4.10249 81.3567
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 0.957324 0.000311226
1 104.484 0.0552919
Memory usage per processor = 10.7951 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.5903396 450.00268 0.22908091 9.3496822 1000000 948.53777 0
500 -3.1308284 302.87516 0.31852936 8.7228753 945961.48 -1250.0622 32.762632
1000 -3.2135069 299.78487 0.34026762 8.618687 898594.67 -816.8599 28.835968
1500 -3.2408919 299.31413 0.34237664 8.5893872 866216.48 -496.30803 30.27954
SHAKE stats (type/ave/delta) on step 2000
1 0.957189 6.77276e-06
1 104.52 0.000459745
2000 -3.2548512 299.54011 0.34350202 8.5744754 846397.03 -235.94776 29.114798
2500 -3.2636044 299.34894 0.34574565 8.5634948 835151.48 -31.295747 29.387608
3000 -3.2697511 298.28636 0.34785467 8.5551984 830776.42 59.254182 28.06448
3500 -3.2715409 300.38451 0.34596334 8.555233 828328.7 66.092433 28.514151
SHAKE stats (type/ave/delta) on step 4000
1 0.957199 4.88987e-06
1 104.52 0.000548489
4000 -3.2644235 301.75849 0.34575269 8.5626387 830015.44 73.234123 28.216187
4500 -3.2667738 300.08217 0.34431253 8.5617113 828725.56 40.199104 29.081006
5000 -3.2667602 300.97714 0.34681903 8.5592106 827745.64 126.40778 27.863006
5500 -3.2640393 299.14814 0.34027613 8.5685232 830760.94 -79.094555 28.25649
SHAKE stats (type/ave/delta) on step 6000
1 0.957201 5.16561e-06
1 104.52 0.000571963
6000 -3.2680213 298.90605 0.34645088 8.558335 829145.11 72.900664 27.682138
6500 -3.2637611 300.64179 0.33918868 8.570067 830171.57 -94.022409 28.857355
7000 -3.2591136 299.25693 0.34374418 8.5700362 829602.84 60.194699 28.271502
7500 -3.2623351 300.36786 0.34070833 8.5699122 829609.52 -42.176872 28.691686
SHAKE stats (type/ave/delta) on step 8000
1 0.957199 3.94755e-06
1 104.52 0.000463992
8000 -3.2638392 299.9633 0.34079794 8.5681413 829840.99 -29.828751 27.934723
8500 -3.2672834 299.33757 0.34504224 8.5605151 829908.63 38.57336 27.789627
9000 -3.2703758 299.92284 0.33976181 8.5628563 828818.41 -101.01572 28.277734
9500 -3.2666488 299.0823 0.34447935 8.5616615 830733.15 -8.5255034 28.055458
SHAKE stats (type/ave/delta) on step 10000
1 0.957206 4.4919e-06
1 104.52 0.000515663
10000 -3.2640714 297.17777 0.34265438 8.5661165 829731.65 -2.6214619 28.31163
Loop time of 348.763 on 192 procs (64 MPI x 3 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 170.61 (48.9185)
Bond time (%) = 0.0251774 (0.00721906)
Kspce time (%) = 64.173 (18.4002)
Neigh time (%) = 57.2283 (16.4089)
Comm time (%) = 23.5579 (6.7547)
Outpt time (%) = 0.00743095 (0.00213066)
Other time (%) = 33.1615 (9.50833)
FFT time (% of Kspce) = 23.1067 (36.0069)
FFT Gflps 3d (1d only) = 4.34141 82.0643
Nlocal: 1312.5 ave 1350 max 1269 min
Histogram: 1 1 8 9 10 8 10 10 4 3
Nghost: 16958.9 ave 17052 max 16848 min
Histogram: 1 2 7 9 11 10 6 8 6 4
Neighs: 1.24954e+06 ave 1.33149e+06 max 1.1956e+06 min
Histogram: 6 6 7 15 12 8 2 7 0 1
Total # of neighbors = 79970498
Ave neighs/atom = 952.03
Ave special neighs/atom = 2
Neighbor list builds = 890
Dangerous builds = 0
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