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lammps/bench-nsf/wat/log.wat-cpu-4m1t-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 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 4 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 = 2744 900 1764
Memory usage per processor = 11.1212 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 6.9626537
20 -1.1179164 300 0.8032691 10.22405 1000000 29606.375 4.8208174
30 -1.5507008 300 0.45424719 10.075517 1000000 -7356.6579 3.5366507
40 -2.0194178 300 0.28674777 9.8007062 1000000 -30757.85 3.6107625
50 -2.2607393 300 0.25541475 9.6424539 1000000 3763.8139 3.1973011
60 -2.3102117 300 0.25222143 9.5946579 1000000 -14375.841 2.6140913
70 -2.3399117 300 0.25055131 9.5696298 1000000 -6039.3247 2.3981949
80 -2.4564331 300 0.24239689 9.4584968 1000000 17982.743 2.8828223
90 -2.6358562 300 0.2192446 9.3021421 1000000 -8463.1743 3.0882737
94 -2.6485731 300 0.21842822 9.3017055 1000000 1114.2325 1.9349451
Loop time of 29.0047 on 64 procs (64 MPI x 1 OpenMP) for 94 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.64847543673 -2.64857313811
Force two-norm initial, final = 2.24428e+07 936.617
Force max component initial, final = 305690 6.31628
Final line search alpha, max atom move = 7.95764e-06 5.02626e-05
Iterations, force evaluations = 94 491
Pair time (%) = 23.6315 (81.4748)
Bond time (%) = 0.0967002 (0.333395)
Kspce time (%) = 3.40066 (11.7245)
Neigh time (%) = 0 (0)
Comm time (%) = 1.51899 (5.23704)
Outpt time (%) = 0.00584599 (0.0201553)
Other time (%) = 0.350983 (1.21009)
FFT time (% of Kspce) = 0.179555 (5.28)
FFT Gflps 3d (1d only) = 5.25168 104.547
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 0.95733 0.000275613
1 104.484 0.0463752
Memory usage per processor = 10.794 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.6500156 450.00268 0.21842822 9.3017055 1000000 313.22684 0
500 -3.139422 302.16934 0.32005564 8.7128769 943596.33 -1280.5257 17.397078
1000 -3.2113487 297.94184 0.33639565 8.6248234 896509.88 -847.14302 15.661929
1500 -3.24139 299.50964 0.33969056 8.5915416 864676.37 -538.51833 15.408664
SHAKE stats (type/ave/delta) on step 2000
1 0.957191 4.36907e-06
1 104.52 0.000631446
2000 -3.2545691 299.21753 0.34798301 8.5702076 845573.79 -108.26486 14.718209
2500 -3.2626789 299.26375 0.34217097 8.5679531 836308.54 -137.24052 14.775832
3000 -3.2596846 299.48654 0.34327598 8.5698625 830437.14 59.776171 14.454177
3500 -3.270085 299.41915 0.34583413 8.5569503 828511.27 51.173447 14.566753
SHAKE stats (type/ave/delta) on step 4000
1 0.957197 4.46122e-06
1 104.52 0.00045123
4000 -3.267252 299.5076 0.34103944 8.5645673 828651.14 -34.694559 14.402804
4500 -3.2674533 300.33779 0.34242101 8.5631144 829573.96 -31.360673 14.50027
5000 -3.2598299 298.88738 0.33682936 8.5761502 830240.31 -118.52017 14.416102
5500 -3.2699541 299.30001 0.34137583 8.5614493 828153.53 -52.856232 14.5754
SHAKE stats (type/ave/delta) on step 6000
1 0.957202 4.09327e-06
1 104.52 0.000439383
6000 -3.2638064 301.39766 0.34235265 8.5666102 829815.11 -6.1891605 14.489495
6500 -3.2682134 298.48779 0.34717648 8.5575975 829896.39 74.4746 14.566232
7000 -3.2689961 301.33418 0.34054453 8.5633182 829950.67 -89.72627 14.380736
7500 -3.2707108 299.14756 0.34587625 8.5562818 830254.96 30.773802 14.486709
SHAKE stats (type/ave/delta) on step 8000
1 0.957198 4.69882e-06
1 104.52 0.000456359
8000 -3.2698265 299.81275 0.35104309 8.5520051 828609.28 179.13113 14.273257
8500 -3.2671664 300.0167 0.34425634 8.5614687 827207.15 80.569135 14.491215
9000 -3.271465 299.22997 0.34776512 8.5537536 829479.37 61.802192 14.289394
9500 -3.2670556 298.85759 0.34612432 8.5595206 827582.48 120.42214 14.50124
SHAKE stats (type/ave/delta) on step 10000
1 0.957205 4.04832e-06
1 104.52 0.0004317
10000 -3.2646695 300.01065 0.34174297 8.5664488 830949.02 -49.939835 14.197101
Loop time of 680.368 on 64 procs (64 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 466.158 (68.5156)
Bond time (%) = 0.0323062 (0.00474834)
Kspce time (%) = 82.568 (12.1358)
Neigh time (%) = 53.6699 (7.88837)
Comm time (%) = 37.0424 (5.44446)
Outpt time (%) = 0.0128632 (0.00189063)
Other time (%) = 40.8839 (6.0091)
FFT time (% of Kspce) = 18.9147 (22.908)
FFT Gflps 3d (1d only) = 5.30359 103.707
Nlocal: 1312.5 ave 1352 max 1254 min
Histogram: 1 2 3 2 10 10 18 6 7 5
Nghost: 16931.8 ave 17039 max 16776 min
Histogram: 2 0 1 6 12 12 12 10 5 4
Neighs: 1.2478e+06 ave 1.32417e+06 max 1.1656e+06 min
Histogram: 1 2 6 10 6 19 11 3 5 1
Total # of neighbors = 79859305
Ave neighs/atom = 950.706
Ave special neighs/atom = 2
Neighbor list builds = 887
Dangerous builds = 0
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