forked from lijiext/lammps
update log files for pair style python examples
This commit is contained in:
Axel Kohlmeyer
parent
96f0a82aa5
commit
13e16dc3f1
|
|
@ -0,0 +1,123 @@
|
||||||
|
LAMMPS (4 May 2017)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||||
|
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)
|
||||||
|
1 by 1 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 python 12.0 coul/long 12.0
|
||||||
|
kspace_style pppm 1.0e-6
|
||||||
|
|
||||||
|
pair_coeff * * coul/long
|
||||||
|
pair_coeff * * python potentials.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 = 103823 64000
|
||||||
|
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 python, perpetual, skip from (2)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) pair 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) = 41.05 | 41.05 | 41.05 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 63.3145 on 1 procs for 100 steps with 4500 atoms
|
||||||
|
|
||||||
|
Performance: 0.136 ns/day, 175.874 hours/ns, 1.579 timesteps/s
|
||||||
|
86.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 61.815 | 61.815 | 61.815 | 0.0 | 97.63
|
||||||
|
Bond | 0.000132 | 0.000132 | 0.000132 | 0.0 | 0.00
|
||||||
|
Kspace | 1.2226 | 1.2226 | 1.2226 | 0.0 | 1.93
|
||||||
|
Neigh | 0.21684 | 0.21684 | 0.21684 | 0.0 | 0.34
|
||||||
|
Comm | 0.015175 | 0.015175 | 0.015175 | 0.0 | 0.02
|
||||||
|
Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.00
|
||||||
|
Modify | 0.040088 | 0.040088 | 0.040088 | 0.0 | 0.06
|
||||||
|
Other | | 0.003896 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 4500 ave 4500 max 4500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 21216 ave 21216 max 21216 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 1.44594e+06 ave 1.44594e+06 max 1.44594e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 1445935
|
||||||
|
Ave neighs/atom = 321.319
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:01:05
|
||||||
|
|
@ -0,0 +1,123 @@
|
||||||
|
LAMMPS (4 May 2017)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||||
|
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 python 12.0 coul/long 12.0
|
||||||
|
kspace_style pppm 1.0e-6
|
||||||
|
|
||||||
|
pair_coeff * * coul/long
|
||||||
|
pair_coeff * * python potentials.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 python, perpetual, skip from (2)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) pair 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) = 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 29.6024 on 4 procs for 100 steps with 4500 atoms
|
||||||
|
|
||||||
|
Performance: 0.292 ns/day, 82.229 hours/ns, 3.378 timesteps/s
|
||||||
|
52.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 26.631 | 27.507 | 28.649 | 14.3 | 92.92
|
||||||
|
Bond | 0.00021 | 0.00022675 | 0.000248 | 0.0 | 0.00
|
||||||
|
Kspace | 0.72315 | 1.8708 | 2.7365 | 54.7 | 6.32
|
||||||
|
Neigh | 0.10667 | 0.1067 | 0.10674 | 0.0 | 0.36
|
||||||
|
Comm | 0.045357 | 0.054035 | 0.064607 | 3.6 | 0.18
|
||||||
|
Output | 0.000424 | 0.00086625 | 0.002189 | 0.0 | 0.00
|
||||||
|
Modify | 0.056602 | 0.056667 | 0.056763 | 0.0 | 0.19
|
||||||
|
Other | | 0.006337 | | | 0.02
|
||||||
|
|
||||||
|
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: 361484 ave 376583 max 347969 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1445935
|
||||||
|
Ave neighs/atom = 321.319
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:30
|
||||||
Loading…
Reference in New Issue