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lammps/bench-nsf/wat/log.wat-cpu-2m1t-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)
2 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)
2 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 = 4508 2592 2898
Memory usage per processor = 18.4486 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 3.6090074
20 -1.1179164 300 0.8032691 10.22405 1000000 29606.373 2.489177
30 -1.5509563 300 0.45424197 10.075516 1000000 -7423.8066 1.8151436
40 -1.9048962 300 0.34163938 9.9089724 1000000 21904.213 1.5779026
50 -2.0410421 300 0.30734178 9.7971856 1000000 -3316.1755 1.3638678
60 -2.1998284 300 0.27822259 9.6553302 1000000 -13625.57 1.4801435
66 -2.3227669 300 0.26499006 9.57526 1000000 5736.9544 1.3767578
Loop time of 37.0813 on 32 procs (32 MPI x 1 OpenMP) for 66 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.32254902896 -2.32276691865
Force two-norm initial, final = 2.24428e+07 1845.02
Force max component initial, final = 305690 21.4166
Final line search alpha, max atom move = 1.11736e-05 0.000239301
Iterations, force evaluations = 66 322
Pair time (%) = 32.9621 (88.8916)
Bond time (%) = 0.136127 (0.367105)
Kspce time (%) = 2.73817 (7.38423)
Neigh time (%) = 0 (0)
Comm time (%) = 0.989518 (2.66851)
Outpt time (%) = 0.00284141 (0.00766264)
Other time (%) = 0.252492 (0.680916)
FFT time (% of Kspce) = 0.129861 (4.74263)
FFT Gflps 3d (1d only) = 5.09839 57.0403
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 0.957304 0.000438267
1 104.495 0.121899
Memory usage per processor = 17.9467 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3239777 450.00268 0.26499006 9.57526 1000000 3527.5065 0
500 -3.0962652 308.71755 0.30925061 8.7664608 960246.12 -1344.4038 9.3028824
1000 -3.2016136 300.63342 0.33539441 8.6355132 909545.5 -948.84306 8.3242074
1500 -3.2315678 301.72813 0.34151057 8.5994441 874271.62 -547.57245 8.2171744
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.30233e-06
1 104.52 0.000457228
2000 -3.2486061 299.34219 0.34409774 8.579929 852007.06 -265.50881 7.7808451
2500 -3.2601528 300.3474 0.34957541 8.5630088 838938.16 -1.3487927 7.7433552
3000 -3.2665684 299.6585 0.34411498 8.5620996 832481.21 -42.448223 7.4680077
3500 -3.271971 298.00571 0.34333145 8.5575349 829386.81 -38.178107 7.66957
SHAKE stats (type/ave/delta) on step 4000
1 0.957204 5.12866e-06
1 104.52 0.000501986
4000 -3.2647263 301.07912 0.34262665 8.5654001 829226.41 8.6336609 7.5299037
4500 -3.2632805 298.15346 0.3416206 8.5678716 829945.26 -37.627042 7.591555
5000 -3.2699406 299.73167 0.3425715 8.5603734 830093.23 -44.376924 7.5108743
5500 -3.2655687 299.4362 0.34321671 8.5640986 830278.79 -10.932431 7.6383516
SHAKE stats (type/ave/delta) on step 6000
1 0.957202 5.07741e-06
1 104.52 0.000489472
6000 -3.2628744 299.25074 0.3433478 8.5664496 827301.21 83.705623 7.4669376
6500 -3.262391 302.36281 0.34118986 8.5692955 828438.18 29.856275 7.6182154
7000 -3.2692297 300.3705 0.34426664 8.5592357 829218.78 -6.6478899 7.5011138
7500 -3.2699043 299.73219 0.34159124 8.561472 827435.42 -24.703642 7.6509182
SHAKE stats (type/ave/delta) on step 8000
1 0.957203 4.52433e-06
1 104.52 0.000442965
8000 -3.2660396 299.86751 0.34768695 8.5591572 828671.8 133.70261 7.4789214
8500 -3.2689368 298.64015 0.34635692 8.5575048 829131.65 57.853923 7.6914473
9000 -3.2644844 300.66278 0.3422756 8.5662671 830545.96 -43.522223 7.5419929
9500 -3.2664476 301.78962 0.34548121 8.5607655 828132.13 84.700492 7.6560375
SHAKE stats (type/ave/delta) on step 10000
1 0.957201 3.92964e-06
1 104.52 0.000552835
10000 -3.2651446 301.50552 0.34039595 8.5672481 828965.25 -40.432308 7.4509687
Loop time of 1295.1 on 32 procs (32 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 975.357 (75.311)
Bond time (%) = 0.0362342 (0.00279778)
Kspce time (%) = 110.625 (8.54178)
Neigh time (%) = 113.246 (8.74416)
Comm time (%) = 36.5733 (2.82396)
Outpt time (%) = 0.00886729 (0.000684677)
Other time (%) = 59.2586 (4.57559)
FFT time (% of Kspce) = 19.7279 (17.8332)
FFT Gflps 3d (1d only) = 5.08495 56.7901
Nlocal: 2625 ave 2685 max 2560 min
Histogram: 1 2 2 3 6 7 4 3 2 2
Nghost: 23220.7 ave 23357 max 23102 min
Histogram: 5 1 6 4 2 1 5 3 3 2
Neighs: 2.50155e+06 ave 2.60017e+06 max 2.39737e+06 min
Histogram: 4 2 3 4 2 0 5 6 4 2
Total # of neighbors = 80049529
Ave neighs/atom = 952.971
Ave special neighs/atom = 2
Neighbor list builds = 886
Dangerous builds = 0
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