127 lines
4.1 KiB
Groff
127 lines
4.1 KiB
Groff
LAMMPS (09 Jan 2020)
|
|
#Initialisation
|
|
|
|
units nano
|
|
dimension 3
|
|
boundary p p p
|
|
atom_style full
|
|
comm_modify cutoff 11.0
|
|
neighbor 7.80 bin
|
|
newton on
|
|
|
|
#Read data
|
|
|
|
read_data cnt.data
|
|
orthogonal box = (0 0 0) to (600 600 60)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
500 atoms
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
scanning angles ...
|
|
1 = max angles/atom
|
|
reading bonds ...
|
|
498 bonds
|
|
reading angles ...
|
|
496 angles
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of 1-3 neighbors
|
|
4 = max # of 1-4 neighbors
|
|
6 = max # of special neighbors
|
|
special bonds CPU = 0.000180006 secs
|
|
read_data CPU = 0.00125766 secs
|
|
replicate 1 2 2
|
|
orthogonal box = (0 0 0) to (600 1200 120)
|
|
1 by 1 by 1 MPI processor grid
|
|
2000 atoms
|
|
1992 bonds
|
|
1984 angles
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of 1-3 neighbors
|
|
4 = max # of 1-4 neighbors
|
|
6 = max # of special neighbors
|
|
special bonds CPU = 0.00054121 secs
|
|
replicate CPU = 0.000902414 secs
|
|
|
|
#Force field
|
|
|
|
bond_style harmonic
|
|
bond_coeff 1 268896.77 2.0
|
|
|
|
angle_style harmonic
|
|
angle_coeff 1 46562.17 180.0
|
|
|
|
pair_style mesocnt
|
|
pair_coeff * * 10_10.cnt
|
|
Reading potential file 10_10.cnt with DATE: 2020-01-13
|
|
|
|
#Output
|
|
|
|
thermo 1000
|
|
dump xyz all xyz 1000 cnt.xyz
|
|
|
|
#Simulation setup
|
|
|
|
timestep 1.0e-05
|
|
|
|
#Nose-Hoover thermostat
|
|
fix nvt all nvt temp 300 300 0.001
|
|
run 10000
|
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 10.177
|
|
ghost atom cutoff = 11
|
|
binsize = 5.0885, bins = 118 236 24
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair mesocnt, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
|
|
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
|
|
2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757
|
|
3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539
|
|
4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866
|
|
5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738
|
|
6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986
|
|
7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796
|
|
8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885
|
|
9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197
|
|
10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903
|
|
Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
|
|
|
|
Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38
|
|
Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57
|
|
Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03
|
|
Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05
|
|
Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52
|
|
Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37
|
|
Other | | 0.04409 | | | 1.09
|
|
|
|
Nlocal: 2000 ave 2000 max 2000 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 0 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 13320 ave 13320 max 13320 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 13320
|
|
Ave neighs/atom = 6.66
|
|
Ave special neighs/atom = 5.952
|
|
Neighbor list builds = 1
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:05
|