Homec4science
Diffusion lammps (runner) Browse

lammps/bench-nsf/wat/log.wat-omp-2m4t-abe
4d6eaa7c83ferunner

Last Change
Raw File

log.wat-omp-2m4t-abe
View Options

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
using 4 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)
2 by 4 by 4 processor grid
using 4 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 = 4508 2592 2898
Memory usage per processor = 18.4497 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 1.6557273
20 -1.1179164 300 0.8032691 10.22405 1000000 29606.373 1.1379302
30 -1.5509555 300 0.45424199 10.075516 1000000 -7423.6079 0.82989148
40 -1.842504 300 0.36574887 9.9471726 1000000 13116.398 0.66441006
50 -1.9656675 300 0.32472011 9.8391607 1000000 -24644.664 0.59466973
60 -2.1673192 300 0.28421813 9.6777068 1000000 328.96634 0.66479863
70 -2.3585759 300 0.26092003 9.5341823 1000000 -15788.446 0.69973359
80 -2.474237 300 0.24801709 9.4438542 1000000 5540.1563 0.71186456
82 -2.4749929 300 0.24795996 9.4428466 1000000 2896.4456 0.39950158
Loop time of 107.132 on 128 procs (32 MPI x 4 OpenMP) for 82 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.47483828454 -2.47499286257
Force two-norm initial, final = 2.24428e+07 1263.6
Force max component initial, final = 305690 16.6575
Final line search alpha, max atom move = 8.96517e-06 0.000149338
Iterations, force evaluations = 82 426
Pair time (%) = 84.0951 (78.497)
Bond time (%) = 0.163778 (0.152875)
Kspce time (%) = 21.2421 (19.8281)
Neigh time (%) = 0 (0)
Comm time (%) = 1.25811 (1.17436)
Outpt time (%) = 0.00303371 (0.00283176)
Other time (%) = 0.369457 (0.344863)
FFT time (% of Kspce) = 0.148169 (0.697525)
FFT Gflps 3d (1d only) = 5.55168 58.178
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 0.957323 0.000347358
1 104.484 0.0551939
Memory usage per processor = 17.9479 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.4764433 450.00268 0.24795996 9.4428466 1000000 2123.7086 0
500 -3.1158335 304.71724 0.31007741 8.7462831 952937.2 -1416.2448 22.034695
1000 -3.2043701 299.42711 0.33422091 8.6339443 903214.38 -965.9076 19.910049
1500 -3.2335759 299.04776 0.33857563 8.6005194 869883.97 -580.82682 19.889371
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 3.80237e-06
1 104.52 0.000422188
2000 -3.2542167 299.11218 0.34475303 8.5736651 849556.09 -240.3717 18.834836
2500 -3.2617014 300.59725 0.34290613 8.568331 836994.23 -87.79442 19.258557
3000 -3.2682656 299.90896 0.3419217 8.5627416 830824.18 -53.458706 18.426285
3500 -3.2706973 303.55459 0.34514368 8.5570477 829667.45 11.898902 18.773849
SHAKE stats (type/ave/delta) on step 4000
1 0.957204 4.01469e-06
1 104.52 0.000575659
4000 -3.2648004 297.90158 0.34360291 8.5644303 831455.95 -14.947445 18.159439
4500 -3.2658256 300.91322 0.33719168 8.5699135 828489.85 -114.43327 18.670456
5000 -3.2664661 300.5418 0.34429217 8.5620269 830074.92 11.417836 18.157512
5500 -3.2625953 299.75199 0.34238856 8.5677975 830211.7 -4.7192098 18.829033
SHAKE stats (type/ave/delta) on step 6000
1 0.957203 4.15638e-06
1 104.52 0.000435861
6000 -3.265191 299.78018 0.34128662 8.5663912 829798.29 -47.706214 17.985081
6500 -3.2662736 300.78899 0.33933524 8.5673116 827433.78 -43.469999 18.710708
7000 -3.2616829 299.91765 0.3489374 8.5621311 828856.35 186.79348 18.177841
7500 -3.2742984 300.06924 0.34942564 8.5491365 829670.28 72.949622 17.989041
SHAKE stats (type/ave/delta) on step 8000
1 0.957197 4.38933e-06
1 104.52 0.000429796
8000 -3.2632098 299.94533 0.34198845 8.5677264 827357.03 54.915046 17.837642
8500 -3.2671359 301.06383 0.34736273 8.5584137 829400.35 112.44328 18.877343
9000 -3.2639185 299.45474 0.34206099 8.5669158 830762.2 -38.865117 18.220841
9500 -3.2685372 301.175 0.34824291 8.5559867 829870.67 95.550667 18.789218
SHAKE stats (type/ave/delta) on step 10000
1 0.957201 4.78911e-06
1 104.52 0.000500914
10000 -3.2642905 301.74124 0.33868422 8.5698581 829948.1 -82.622233 18.329069
Loop time of 533.299 on 128 procs (32 MPI x 4 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 249.691 (46.8201)
Bond time (%) = 0.040384 (0.00757249)
Kspce time (%) = 76.8926 (14.4183)
Neigh time (%) = 109.587 (20.5489)
Comm time (%) = 36.9872 (6.93554)
Outpt time (%) = 0.00728879 (0.00136674)
Other time (%) = 60.0935 (11.2683)
FFT time (% of Kspce) = 18.5586 (24.1358)
FFT Gflps 3d (1d only) = 5.40534 58.2606
Nlocal: 2625 ave 2681 max 2571 min
Histogram: 2 1 3 7 3 6 5 1 1 3
Nghost: 23259.7 ave 23359 max 23150 min
Histogram: 3 2 1 3 4 6 5 3 3 2
Neighs: 2.49868e+06 ave 2.6476e+06 max 2.39475e+06 min
Histogram: 2 5 1 6 9 4 2 2 0 1
Total # of neighbors = 79957724
Ave neighs/atom = 951.878
Ave special neighs/atom = 2
Neighbor list builds = 891
Dangerous builds = 0
c4science · Help