forked from lijiext/lammps
123 lines
4.1 KiB
Groff
123 lines
4.1 KiB
Groff
LAMMPS (4 May 2017)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
units real
|
|
atom_style full
|
|
|
|
read_data data.spce
|
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
|
2 by 2 by 1 MPI processor grid
|
|
reading atoms ...
|
|
4500 atoms
|
|
scanning bonds ...
|
|
2 = max bonds/atom
|
|
scanning angles ...
|
|
1 = max angles/atom
|
|
reading bonds ...
|
|
3000 bonds
|
|
reading angles ...
|
|
1500 angles
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
|
kspace_style pppm 1.0e-6
|
|
|
|
pair_coeff * * coul/long
|
|
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
|
|
|
bond_style harmonic
|
|
angle_style harmonic
|
|
dihedral_style none
|
|
improper_style none
|
|
|
|
bond_coeff 1 1000.00 1.000
|
|
angle_coeff 1 100.0 109.47
|
|
|
|
special_bonds lj/coul 0.0 0.0 1.0
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
neighbor 2.0 bin
|
|
|
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
|
0 = # of size 2 clusters
|
|
0 = # of size 3 clusters
|
|
0 = # of size 4 clusters
|
|
1500 = # of frozen angles
|
|
fix 2 all nvt temp 300.0 300.0 100.0
|
|
|
|
thermo 10
|
|
run 100
|
|
PPPM initialization ...
|
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|
G vector (1/distance) = 0.279652
|
|
grid = 40 40 40
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.000394674
|
|
estimated relative force accuracy = 1.18855e-06
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 34263 16000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 14
|
|
ghost atom cutoff = 14
|
|
binsize = 7, bins = 6 6 6
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair coul/long, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
(2) pair python, perpetual, skip from (1)
|
|
attributes: half, newton on
|
|
pair build: skip
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0 -16692.369 0 -16692.369 -1289.222
|
|
10 120.56861 -17769.719 0 -16691.902 -4082.7098
|
|
20 136.08014 -17884.591 0 -16668.109 -5140.7824
|
|
30 136.97316 -17874.351 0 -16649.887 -5351.3571
|
|
40 153.37285 -18001.493 0 -16630.424 -5227.0601
|
|
50 167.70414 -18105.435 0 -16606.252 -4473.2089
|
|
60 163.08253 -18037.29 0 -16579.422 -3295.8963
|
|
70 169.60395 -18067.078 0 -16550.912 -2615.7026
|
|
80 182.94811 -18155.978 0 -16520.523 -2393.3156
|
|
90 191.29902 -18197.887 0 -16487.779 -2242.7104
|
|
100 194.70949 -18195.021 0 -16454.425 -1955.2916
|
|
Loop time of 6.588 on 4 procs for 100 steps with 4500 atoms
|
|
|
|
Performance: 1.311 ns/day, 18.300 hours/ns, 15.179 timesteps/s
|
|
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 5.3756 | 5.5417 | 5.8745 | 8.3 | 84.12
|
|
Bond | 0.0001049 | 0.00013965 | 0.0001812 | 0.0 | 0.00
|
|
Kspace | 0.54765 | 0.87786 | 1.042 | 20.8 | 13.33
|
|
Neigh | 0.072695 | 0.072884 | 0.072973 | 0.0 | 1.11
|
|
Comm | 0.04138 | 0.043576 | 0.045475 | 0.7 | 0.66
|
|
Output | 0.00041032 | 0.00043947 | 0.00052142 | 0.0 | 0.01
|
|
Modify | 0.047381 | 0.047567 | 0.047745 | 0.1 | 0.72
|
|
Other | | 0.003845 | | | 0.06
|
|
|
|
Nlocal: 1125 ave 1154 max 1092 min
|
|
Histogram: 1 0 0 0 1 0 0 1 0 1
|
|
Nghost: 12256.2 ave 12296 max 12213 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
Neighs: 650440 ave 678828 max 626375 min
|
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
|
|
|
Total # of neighbors = 2601762
|
|
Ave neighs/atom = 578.169
|
|
Ave special neighs/atom = 2
|
|
Neighbor list builds = 3
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:06
|