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lammps/bench-nsf/wat/log.wat-omp2-ranger
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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 159414.92 2.9128287
20 -1.1179165 300 0.80326912 10.22405 1000000 29606.337 2.0275216
30 -1.5562003 300 0.45411855 10.075443 1000000 -9119.0134 1.4784462
40 -1.9138793 300 0.31734815 9.8619184 1000000 -44759.543 1.347377
50 -2.1241512 300 0.27255474 9.7575031 1000000 3256.7528 1.1074312
60 -2.3061031 300 0.26015786 9.5694866 1000000 12860.176 1.2671963
70 -2.4957116 300 0.24095923 9.4258783 1000000 5011.0235 1.2451748
76 -2.539187 300 0.23618957 9.391748 1000000 2736.3432 1.0398651
Loop time of 53.2733 on 128 procs (64 MPI x 2 OpenMP) for 76 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.53907575871 -2.53918696552
Force two-norm initial, final = 2.24428e+07 1188.75
Force max component initial, final = 305690 11.7349
Final line search alpha, max atom move = 7.37936e-06 8.65957e-05
Iterations, force evaluations = 76 377
Pair time (%) = 33.6948 (63.249)
Bond time (%) = 0.0692734 (0.130034)
Kspce time (%) = 17.9067 (33.6129)
Neigh time (%) = 0 (0)
Comm time (%) = 1.33318 (2.50254)
Outpt time (%) = 0.00150752 (0.00282978)
Other time (%) = 0.267821 (0.502731)
FFT time (% of Kspce) = 0.116836 (0.652472)
FFT Gflps 3d (1d only) = 6.52537 17.7405
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 0.957321 0.00038299
1 104.488 0.0502777
Memory usage per processor = 10.795 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.5405107 450.00268 0.23618957 9.391748 1000000 1443.7086 0
500 -3.1231084 303.45585 0.31456224 8.7344536 949367.17 -1313.4303 21.701378
1000 -3.2067936 298.83842 0.33867656 8.6270286 900555.94 -824.64708 19.723327
1500 -3.2349445 301.77668 0.34451946 8.5930151 868531.77 -405.12091 19.549637
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.24063e-06
1 104.52 0.000418806
2000 -3.2509619 299.03088 0.34258231 8.5793541 846977.96 -221.77284 18.364956
2500 -3.2674017 298.5652 0.3525759 8.5528687 836400.05 71.140374 18.579059
3000 -3.2681734 298.73614 0.34282032 8.5620346 830359.53 -43.792163 17.933141
3500 -3.2682382 300.96095 0.34358479 8.5610515 828447.86 3.4619844 18.481774
SHAKE stats (type/ave/delta) on step 4000
1 0.957205 4.67364e-06
1 104.52 0.000423651
4000 -3.2684823 299.87834 0.34391778 8.5603859 827011.2 53.6612 17.686032
4500 -3.2697974 299.70333 0.34154439 8.5616542 830417.14 -95.205877 18.24102
5000 -3.2663896 299.43464 0.34941574 8.5568399 829009.59 154.54542 17.461533
5500 -3.2642083 300.12219 0.3434933 8.5653008 831582.25 -16.688844 17.924814
SHAKE stats (type/ave/delta) on step 6000
1 0.957203 4.70421e-06
1 104.52 0.000529967
6000 -3.2606444 298.98227 0.34280643 8.5693502 828830.01 72.368127 17.600552
6500 -3.2649114 300.74485 0.33837776 8.569518 828987.96 -97.36463 18.280469
7000 -3.2668713 299.66725 0.34070921 8.5652016 829745.69 -72.343772 17.597617
7500 -3.2647258 300.15992 0.34151664 8.5666354 828462.54 -13.375696 18.310871
SHAKE stats (type/ave/delta) on step 8000
1 0.957204 4.79803e-06
1 104.52 0.000474192
8000 -3.2564712 299.04483 0.34257389 8.5736283 828986.12 70.015666 17.59121
8500 -3.270438 300.57785 0.34235161 8.559969 828073.5 -28.132529 18.17117
9000 -3.2672266 300.08449 0.33759004 8.5680452 829510.33 -148.04567 17.484053
9500 -3.2659451 300.90133 0.3434022 8.5635038 828743.73 58.934955 18.16624
SHAKE stats (type/ave/delta) on step 10000
1 0.957196 5.38986e-06
1 104.52 0.000583094
10000 -3.264276 301.2208 0.34360131 8.5650111 827622.67 70.50086 17.551388
Loop time of 547.277 on 128 procs (64 MPI x 2 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 322.501 (58.9283)
Bond time (%) = 0.0492301 (0.00899546)
Kspce time (%) = 75.6074 (13.8152)
Neigh time (%) = 63.8359 (11.6643)
Comm time (%) = 42.301 (7.72937)
Outpt time (%) = 0.00394313 (0.000720499)
Other time (%) = 42.9783 (7.85312)
FFT time (% of Kspce) = 15.647 (20.6951)
FFT Gflps 3d (1d only) = 6.41117 68.2405
Nlocal: 1312.5 ave 1348 max 1274 min
Histogram: 3 2 5 8 9 10 14 6 5 2
Nghost: 16952.4 ave 17028 max 16840 min
Histogram: 1 2 3 7 7 12 8 11 7 6
Neighs: 1.2527e+06 ave 1.31556e+06 max 1.17873e+06 min
Histogram: 1 1 5 9 11 12 10 10 3 2
Total # of neighbors = 80172939
Ave neighs/atom = 954.44
Ave special neighs/atom = 2
Neighbor list builds = 890
Dangerous builds = 0
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