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lammps/examples/USER/cg-cmm/peg-verlet/log.pegc12e8
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log.pegc12e8
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LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 1 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
40140 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
13284 bonds
reading angles ...
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 12.4188 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 8.6552 (sec) ----------------
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
---------------- Step 400 ----- CPU = 17.5807 (sec) ----------------
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
---------------- Step 600 ----- CPU = 28.1043 (sec) ----------------
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
---------------- Step 800 ----- CPU = 40.5132 (sec) ----------------
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
---------------- Step 1000 ----- CPU = 52.8166 (sec) ----------------
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79
Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88
Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42
Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27
Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00
Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12
Other | | 0.2731 | | | 0.52
Nlocal: 20070 ave 20109 max 20031 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20234 ave 20281 max 20187 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 5691680
Ave neighs/atom = 141.796
Ave special neighs/atom = 1.26861
Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
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