128 lines
5.1 KiB
Groff
128 lines
5.1 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
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 2 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
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 5 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 18
|
|
ghost atom cutoff = 18
|
|
binsize = 9, bins = 15 15 45
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/sdk, 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) = 15.87 | 15.87 | 15.87 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 = 3.0107 (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 = 6.1324 (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 = 9.3443 (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 = 12.5388 (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 = 15.7416 (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 15.7417 on 4 procs for 1000 steps with 40140 atoms
|
|
|
|
Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 timesteps/s
|
|
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 13.591 | 13.612 | 13.626 | 0.4 | 86.47
|
|
Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47
|
|
Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79
|
|
Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65
|
|
Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00
|
|
Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13
|
|
Other | | 0.07576 | | | 0.48
|
|
|
|
Nlocal: 10035 ave 10098 max 10004 min
|
|
Histogram: 2 0 1 0 0 0 0 0 0 1
|
|
Nghost: 14546.5 ave 14564 max 14503 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
|
Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min
|
|
Histogram: 1 1 0 1 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
|
|
|
|
Total wall time: 0:00:15
|