110 lines
4.2 KiB
Groff
110 lines
4.2 KiB
Groff
LAMMPS (2 Aug 2018)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Point dipoles in a 2d box
|
|
|
|
units lj
|
|
atom_style charge
|
|
|
|
read_data data.hammersley_shphere
|
|
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
|
|
2 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
1000 atoms
|
|
change_box all boundary f f f
|
|
|
|
velocity all create 1.5 49893
|
|
|
|
neighbor 1.0 bin
|
|
neigh_modify delay 0
|
|
|
|
fix 1 all nve
|
|
|
|
# LAMMPS computes pairwise and long-range Coulombics
|
|
|
|
#pair_style coul/long 3.0
|
|
#pair_coeff * *
|
|
#kspace_style pppm 1.0e-3
|
|
|
|
# Scafacos computes entire long-range Coulombics
|
|
# use dummy pair style to perform atom sorting
|
|
|
|
pair_style zero 1.0
|
|
pair_coeff * *
|
|
|
|
#fix 2 all scafacos p3m tolerance field 0.001
|
|
|
|
kspace_style scafacos fmm 0.001
|
|
kspace_modify scafacos tolerance energy_rel
|
|
kspace_modify scafacos fmm_tuning 1
|
|
ScaFaCoS setting fmm inhomogen tuning ...
|
|
|
|
timestep 0.005
|
|
thermo 1
|
|
|
|
run 20
|
|
Setting up ScaFaCoS with solver fmm ...
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 2
|
|
ghost atom cutoff = 2
|
|
binsize = 1, bins = 102 102 102
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 1.5 -0.62417141 0 1.6235786 0.0015676581
|
|
1 18.780412 -10.770009 0 17.372438 0.016719188
|
|
2 65.294131 -11.084501 0 86.758754 0.06035827
|
|
3 121.92555 -7.0612033 0 175.64423 0.1140457
|
|
4 185.71165 -5.8781334 0 272.41077 0.17455524
|
|
5 286.28339 -4.3800108 0 424.61565 0.26911306
|
|
6 481.28097 -4.3052012 0 716.89433 0.45262045
|
|
7 487.26022 -3.8672741 0 726.29216 0.45830216
|
|
8 493.65478 -3.0242687 0 736.71742 0.46443761
|
|
9 495.66203 -3.4336343 0 739.31592 0.46613014
|
|
10 498.41831 -2.8837072 0 743.99613 0.46887706
|
|
11 499.20944 -2.7724783 0 745.29287 0.46966875
|
|
12 500.97345 -2.8281484 0 747.88057 0.47126462
|
|
13 507.46412 -2.7752775 0 757.65971 0.47728761
|
|
14 525.35729 -2.5749814 0 784.67292 0.49422171
|
|
15 563.9578 -2.9982381 0 842.09253 0.53043696
|
|
16 645.47602 -2.5519203 0 964.69389 0.60730795
|
|
17 647.09276 -2.2568468 0 967.41166 0.60891914
|
|
18 647.12596 -2.2791003 0 967.43915 0.60900309
|
|
19 647.24862 -2.2495226 0 967.65253 0.60908339
|
|
20 647.51175 -2.0239179 0 968.27244 0.60932598
|
|
Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms
|
|
|
|
Performance: 15174.000 tau/day, 35.125 timesteps/s
|
|
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04
|
|
Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66
|
|
Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57
|
|
Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55
|
|
Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12
|
|
Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02
|
|
Other | | 0.0002268 | | | 0.04
|
|
|
|
Nlocal: 125 ave 137 max 111 min
|
|
Histogram: 1 1 0 0 0 2 2 1 0 1
|
|
Nghost: 768.875 ave 788 max 761 min
|
|
Histogram: 4 0 2 0 0 0 1 0 0 1
|
|
Neighs: 30542.8 ave 48077 max 10011 min
|
|
Histogram: 1 1 1 0 1 1 0 0 0 3
|
|
|
|
Total # of neighbors = 244342
|
|
Ave neighs/atom = 244.342
|
|
Neighbor list builds = 19
|
|
Dangerous builds = 18
|
|
Total wall time: 0:00:01
|