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lammps/bench-nsf/wat/log.wat-omp-4m2t-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 4 processor grid
using 2 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 2 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 = 11.1222 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 3.6491038
20 -1.1179164 300 0.8032691 10.22405 1000000 29606.375 2.5097497
30 -1.5507023 300 0.45424716 10.075517 1000000 -7357.0463 1.8316293
40 -2.011192 300 0.30367655 9.8396931 1000000 24327.457 1.6912776
50 -2.2249121 300 0.27088107 9.6638087 1000000 2671.1052 1.5989485
60 -2.2468709 300 0.26841829 9.6382943 1000000 12309.013 1.203892
69 -2.3580008 300 0.25830015 9.54722 1000000 5120.0866 1.3403897
Loop time of 39.3724 on 128 procs (64 MPI x 2 OpenMP) for 69 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.35780550126 -2.35800080801
Force two-norm initial, final = 2.24428e+07 1269.18
Force max component initial, final = 305690 14.544
Final line search alpha, max atom move = 6.06519e-06 8.82124e-05
Iterations, force evaluations = 69 345
Pair time (%) = 28.4634 (72.2927)
Bond time (%) = 0.0675714 (0.171621)
Kspce time (%) = 9.40752 (23.8937)
Neigh time (%) = 0 (0)
Comm time (%) = 1.11773 (2.83888)
Outpt time (%) = 0.00391128 (0.00993406)
Other time (%) = 0.312275 (0.793132)
FFT time (% of Kspce) = 0.130367 (1.38577)
FFT Gflps 3d (1d only) = 5.30946 106.26
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 0.957307 0.000361457
1 104.486 0.0568153
Memory usage per processor = 10.795 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3593207 450.00268 0.25830015 9.54722 1000000 3151.5815 0
500 -3.1021733 307.8831 0.31080631 8.759028 958540.46 -1360.6369 27.141327
1000 -3.1953824 299.41976 0.33974601 8.6373575 907447.79 -797.88068 25.114999
1500 -3.2363901 299.0472 0.34131293 8.5949139 872681.04 -589.33611 24.406801
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.61282e-06
1 104.52 0.000500649
2000 -3.252339 300.37078 0.3442084 8.5760103 850048.98 -272.68749 23.473221
2500 -3.2586429 299.46467 0.34263538 8.571589 838525.49 -109.94023 23.294422
3000 -3.2642178 298.93855 0.34180545 8.5668119 832132.82 -67.84865 23.083634
3500 -3.2666127 299.53354 0.34675772 8.5594725 828114.1 111.73338 23.218648
SHAKE stats (type/ave/delta) on step 4000
1 0.957203 4.13229e-06
1 104.52 0.00053257
4000 -3.263014 300.66737 0.34230522 8.5674172 829061.83 12.235671 22.587759
4500 -3.2660103 300.39799 0.34294287 8.5639841 829162.56 12.672222 22.890204
5000 -3.2627183 299.78685 0.34468773 8.5654311 829727.76 58.268801 22.712938
5500 -3.2721581 301.56433 0.34140655 8.5593109 829126.44 -85.133863 23.077466
SHAKE stats (type/ave/delta) on step 6000
1 0.957199 5.15173e-06
1 104.52 0.000617602
6000 -3.2638234 298.86133 0.34534536 8.5637792 828653.8 105.34885 22.662989
6500 -3.2638702 300.24949 0.34023197 8.5685053 827957.61 -13.497982 22.85593
7000 -3.2689409 301.37257 0.34120161 8.5627888 828807.23 -52.873803 22.639894
7500 -3.2683828 299.7984 0.34293963 8.5615918 828628.21 3.6549021 23.065901
SHAKE stats (type/ave/delta) on step 8000
1 0.957201 4.30331e-06
1 104.52 0.000586787
8000 -3.2619672 300.04239 0.34106275 8.5699208 829603.05 -4.5153287 22.585558
8500 -3.2696743 299.43794 0.33906492 8.564202 829401.76 -144.97025 23.111381
9000 -3.2688077 299.39904 0.34110494 8.5629108 830788.45 -84.318161 22.450659
9500 -3.2660207 300.58119 0.34057574 8.5663332 831192.59 -93.529493 22.844017
SHAKE stats (type/ave/delta) on step 10000
1 0.957199 4.57678e-06
1 104.52 0.000548639
10000 -3.2708059 299.51425 0.34583859 8.5561192 828072.55 41.605754 22.492655
Loop time of 430.297 on 128 procs (64 MPI x 2 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 228.935 (53.204)
Bond time (%) = 0.03619 (0.00841047)
Kspce time (%) = 63.4341 (14.7419)
Neigh time (%) = 54.2531 (12.6083)
Comm time (%) = 38.8655 (9.03226)
Outpt time (%) = 0.0127926 (0.00297296)
Other time (%) = 44.7601 (10.4021)
FFT time (% of Kspce) = 18.8776 (29.7593)
FFT Gflps 3d (1d only) = 5.31402 104.55
Nlocal: 1312.5 ave 1364 max 1264 min
Histogram: 1 3 10 10 10 14 4 7 4 1
Nghost: 16962.7 ave 17095 max 16808 min
Histogram: 2 4 4 12 6 4 10 15 4 3
Neighs: 1.25204e+06 ave 1.318e+06 max 1.18932e+06 min
Histogram: 2 6 10 11 5 7 9 6 1 7
Total # of neighbors = 80130692
Ave neighs/atom = 953.937
Ave special neighs/atom = 2
Neighbor list builds = 886
Dangerous builds = 0
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