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lammps/bench-nsf/wat/log.wat-cpu-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 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 = 8.86103 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 7.687761
20 -1.1179166 300 0.80326924 10.22405 1000000 29606.046 6.0699941
30 -1.5756342 300 0.45227394 10.073155 1000000 -36041.596 4.4939175
40 -1.8512547 300 0.32692034 9.912253 1000000 -42672.778 3.9753229
50 -2.2087269 300 0.27265297 9.6468897 1000000 -12933.386 4.1260472
60 -2.3507689 300 0.25811741 9.5503197 1000000 19452.687 3.6375463
70 -2.4493415 300 0.24616154 9.4408165 1000000 -38932.01 4.0357584
80 -2.5404193 300 0.23804751 9.3878333 1000000 7711.0613 3.2451549
90 -2.6210028 300 0.22502795 9.3219687 1000000 3467.2601 3.4936497
100 -2.7290021 300 0.20310392 9.2375071 1000000 119.8855 3.5664992
Loop time of 24.1454 on 112 procs (112 MPI x 1 OpenMP) for 100 steps with 84000 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
656.399401959 -2.72581337004 -2.72900214326
Force two-norm initial, final = 2.24428e+07 2744.95
Force max component initial, final = 305690 25.1298
Final line search alpha, max atom move = 1.06042e-05 0.000266483
Iterations, force evaluations = 100 512
Pair time (%) = 15.1676 (62.818)
Bond time (%) = 0.0571719 (0.236782)
Kspce time (%) = 6.28296 (26.0214)
Neigh time (%) = 0 (0)
Comm time (%) = 1.92355 (7.96654)
Outpt time (%) = 0.0113722 (0.0470989)
Other time (%) = 0.702685 (2.91023)
FFT time (% of Kspce) = 0.755454 (12.0239)
FFT Gflps 3d (1d only) = 1.32788 113.973
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 0.957334 0.000465048
1 104.493 0.142273
Memory usage per processor = 8.54327 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.7307735 450.00268 0.20310392 9.2375071 1000000 -567.14281 0
500 -3.1489219 302.9355 0.32480858 8.6984945 941341.87 -1201.4593 21.537363
1000 -3.210628 300.7519 0.33643616 8.6255701 895865.07 -826.66813 20.270151
1500 -3.236304 299.8161 0.33819794 8.5983075 864323.6 -525.68313 19.800863
SHAKE stats (type/ave/delta) on step 2000
1 0.957192 4.23863e-06
1 104.52 0.000444321
2000 -3.2523205 300.88725 0.34175956 8.5787741 846401.64 -227.11487 19.211592
2500 -3.2603048 301.14076 0.34509431 8.5671959 834841.81 0.13388783 19.159271
3000 -3.2666503 300.98463 0.34110468 8.565117 831658.26 -85.288301 18.634192
3500 -3.2672672 302.13981 0.34457914 8.5608138 829885.05 24.574 18.873415
SHAKE stats (type/ave/delta) on step 4000
1 0.957199 4.4485e-06
1 104.52 0.000506013
4000 -3.2716499 301.40861 0.34140704 8.5596845 828853.74 -72.830114 18.645934
4500 -3.2639473 300.61926 0.34300948 8.5658101 829682.73 8.8292941 18.93353
5000 -3.270446 300.97761 0.34231181 8.5600992 828556.99 -30.294374 18.709651
5500 -3.2629553 300.38694 0.34235276 8.567549 831380.03 -36.809063 18.862196
SHAKE stats (type/ave/delta) on step 6000
1 0.957199 4.17935e-06
1 104.52 0.000450251
6000 -3.2636889 297.58573 0.34205675 8.5671283 829806.51 -22.095533 18.890106
6500 -3.2661686 301.10971 0.33799429 8.5685504 828147.41 -95.587685 18.924242
7000 -3.2675537 298.49799 0.34951849 8.5557528 831926.51 76.927991 18.676568
7500 -3.2713501 298.78921 0.3458605 8.5557663 828768.31 46.84045 18.850539
SHAKE stats (type/ave/delta) on step 8000
1 0.957206 4.73043e-06
1 104.52 0.00046902
8000 -3.2650969 299.36051 0.34095251 8.5666993 826965.1 10.985347 18.517429
8500 -3.2645069 299.79938 0.33524969 8.5731853 829903.64 -188.66848 18.710427
9000 -3.2610334 298.42782 0.33904942 8.5728192 831661.95 -102.01548 17.910108
9500 -3.2666867 299.63809 0.34546202 8.5608217 828399.29 77.522735 18.373436
SHAKE stats (type/ave/delta) on step 10000
1 0.957204 4.20518e-06
1 104.52 0.000453942
10000 -3.2667739 300.18545 0.34660209 8.5595824 828637.12 74.964078 18.501546
Loop time of 527.104 on 112 procs (112 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 278.55 (52.8455)
Bond time (%) = 0.0291571 (0.00553158)
Kspce time (%) = 123.679 (23.4638)
Neigh time (%) = 31.8872 (6.04952)
Comm time (%) = 47.3316 (8.97956)
Outpt time (%) = 0.0226973 (0.00430604)
Other time (%) = 45.6038 (8.65178)
FFT time (% of Kspce) = 76.9817 (62.2433)
FFT Gflps 3d (1d only) = 1.30311 110.522
Nlocal: 750 ave 793 max 706 min
Histogram: 1 1 12 14 31 25 9 12 5 2
Nghost: 14251.9 ave 14417 max 14097 min
Histogram: 2 2 8 24 29 19 17 4 4 3
Neighs: 715020 ave 793452 max 662069 min
Histogram: 7 18 13 20 17 20 7 1 5 4
Total # of neighbors = 80082263
Ave neighs/atom = 953.36
Ave special neighs/atom = 2
Neighbor list builds = 887
Dangerous builds = 0
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