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lammps/examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle
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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 sdk
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 = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
---------------- Step 200 ----- CPU = 8.7547 (sec) ----------------
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
---------------- Step 400 ----- CPU = 17.7479 (sec) ----------------
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
---------------- Step 600 ----- CPU = 26.7299 (sec) ----------------
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
---------------- Step 800 ----- CPU = 35.8941 (sec) ----------------
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
---------------- Step 1000 ----- CPU = 45.1542 (sec) ----------------
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27
Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14
Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34
Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49
Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00
Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19
Other | | 0.2571 | | | 0.57
Nlocal: 20070 ave 20100 max 20040 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20230.5 ave 20241 max 20220 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 5686756
Ave neighs/atom = 141.673
Ave special neighs/atom = 1.26861
Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
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