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lammps/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
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log.22Jun2017.peptide.g++.1
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LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
thermo 50
#dump dump1 all atom 100 peptide.dump
timestep 8
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
1 = bond angle
2 = dihedral improper pair
3 = kspace
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
19 = # of size 2 clusters
0 = # of size 3 clusters
3 = # of size 4 clusters
0 = # of size 5 clusters
646 = # of frozen angles
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122
100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011
150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894
200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563
250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359
300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021
350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665
400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811
450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859
500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769
550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227
600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352
650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309
700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651
750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372
800 251.73191 -7315.2457 839.59859 -4972.666 952.56448
850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823
900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166
950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267
1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136
Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80
Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25
Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10
Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48
Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90
Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00
Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10
Other | | 1.289 | | | 0.36
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11191 ave 11191 max 11191 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708610 ave 708610 max 708610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708610
Ave neighs/atom = 353.598
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 200
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:05:57
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