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lammps/bench-nsf/wat/log.wat-omp-7m1t-abe
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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 7 processor grid
using 1 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 7 processor grid
using 1 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 = 2156 540 2352
Memory usage per processor = 8.86198 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 9.131553
20 -1.1179166 300 0.80326924 10.22405 1000000 29606.046 6.3350841
30 -1.575634 300 0.45227405 10.073155 1000000 -36040.286 4.6220141
40 -1.8516977 300 0.3269199 9.9122581 1000000 -42475.325 4.0986225
50 -2.1718558 300 0.27265354 9.6411586 1000000 -25804.878 4.1861498
60 -2.2996855 300 0.26426762 9.5943628 1000000 17574.001 3.3874443
70 -2.5211691 300 0.24274896 9.3995092 1000000 -2701.0738 5.3917627
80 -2.6113154 300 0.22320071 9.3330505 1000000 3973.5898 3.5190178
82 -2.6122506 300 0.2231387 9.3325308 1000000 1008.5229 2.3480907
Loop time of 18.1662 on 112 procs (112 MPI x 1 OpenMP) for 82 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.61209975356 -2.61225061977
Force two-norm initial, final = 2.24428e+07 1461.27
Force max component initial, final = 305690 23.9915
Final line search alpha, max atom move = 2.01913e-05 0.00048442
Iterations, force evaluations = 82 401
Pair time (%) = 11.2198 (61.7616)
Bond time (%) = 0.0447335 (0.246245)
Kspce time (%) = 4.96013 (27.3041)
Neigh time (%) = 0 (0)
Comm time (%) = 1.54321 (8.49493)
Outpt time (%) = 0.00911507 (0.0501759)
Other time (%) = 0.38929 (2.14293)
FFT time (% of Kspce) = 0.639118 (12.8851)
FFT Gflps 3d (1d only) = 1.28707 100.683
Nlocal: 750 ave 818 max 686 min
Histogram: 8 8 4 20 16 20 16 12 4 4
Nghost: 12548.4 ave 12967 max 12124 min
Histogram: 4 8 8 16 20 20 12 12 8 4
Neighs: 591786 ave 653148 max 534460 min
Histogram: 8 16 8 12 8 20 12 16 8 4
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 2352
SHAKE stats (type/ave/delta) on step 0
1 0.957332 0.000419251
1 104.485 0.05927
Memory usage per processor = 8.54422 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.6137839 450.00268 0.2231387 9.3325308 1000000 655.09642 0
500 -3.1349408 303.33467 0.32202336 8.715203 945145.64 -1187.3706 22.662908
1000 -3.2169126 299.76768 0.34126493 8.6144415 897878.96 -811.86648 21.747741
1500 -3.2391996 300.30425 0.34902177 8.5842882 866218.76 -323.85625 21.265236
SHAKE stats (type/ave/delta) on step 2000
1 0.957191 4.66874e-06
1 104.52 0.000442333
2000 -3.2555908 299.83219 0.34552902 8.5718458 847620.22 -196.33944 20.725967
2500 -3.2630588 301.28805 0.34419508 8.565435 836059.46 -63.197454 20.63063
3000 -3.2690347 299.65092 0.34610342 8.5576353 832678.11 20.141711 20.380392
3500 -3.261441 300.82292 0.34345272 8.5680178 830652.87 23.756184 20.526146
SHAKE stats (type/ave/delta) on step 4000
1 0.957196 4.62796e-06
1 104.52 0.000649374
4000 -3.2650472 300.81562 0.34222372 8.5656261 829848.34 -0.22356592 20.202022
4500 -3.2722043 300.77423 0.34623219 8.5545078 828786.42 48.23555 20.439014
5000 -3.2649646 300.53085 0.34137679 8.5664814 829500.18 -8.3591005 20.069957
5500 -3.2665791 299.59714 0.34346412 8.5629958 829791.58 22.755411 20.306441
SHAKE stats (type/ave/delta) on step 6000
1 0.957201 3.93964e-06
1 104.52 0.000485351
6000 -3.2651497 298.49931 0.34419628 8.5635118 830026.78 28.49428 20.103866
6500 -3.2710851 301.0126 0.34839648 8.5533998 827833.36 136.39972 20.317394
7000 -3.2631346 298.3691 0.34095893 8.5688789 829939.01 -51.010111 20.039523
7500 -3.2664629 300.47893 0.3456238 8.5607829 829565.35 63.354967 20.194269
SHAKE stats (type/ave/delta) on step 8000
1 0.957201 3.84949e-06
1 104.52 0.0004958
8000 -3.2661587 299.20693 0.34071037 8.5661054 830214.67 -69.773222 20.066624
8500 -3.2660224 299.1233 0.34346722 8.5633618 828061.59 41.222482 20.184594
9000 -3.2627925 300.7144 0.34653457 8.5633724 829055.16 112.67313 20.134276
9500 -3.2667748 300.52746 0.33731054 8.5688542 831225.52 -185.82553 20.215384
SHAKE stats (type/ave/delta) on step 10000
1 0.957204 4.10772e-06
1 104.52 0.000490225
10000 -3.2726598 300.96561 0.34225319 8.5578252 828064.72 -48.828895 19.945379
Loop time of 488.082 on 112 procs (112 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 244.619 (50.1185)
Bond time (%) = 0.0284541 (0.00582977)
Kspce time (%) = 118.739 (24.3278)
Neigh time (%) = 31.8001 (6.51532)
Comm time (%) = 47.4489 (9.72151)
Outpt time (%) = 0.0238292 (0.00488221)
Other time (%) = 45.422 (9.30622)
FFT time (% of Kspce) = 77.9173 (65.6204)
FFT Gflps 3d (1d only) = 1.28746 109.09
Nlocal: 750 ave 781 max 706 min
Histogram: 2 2 6 4 22 23 21 12 13 7
Nghost: 14283.3 ave 14394 max 14163 min
Histogram: 7 4 14 7 20 14 15 18 10 3
Neighs: 715493 ave 776249 max 629462 min
Histogram: 2 0 4 14 25 16 18 13 12 8
Total # of neighbors = 80135231
Ave neighs/atom = 953.991
Ave special neighs/atom = 2
Neighbor list builds = 886
Dangerous builds = 0
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