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Axel Kohlmeyer authoredAxel Kohlmeyer authored
log.4May17.pair_python_hybrid.g++.1 8.35 KiB
LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass * 1.0
region half block -0.1 4.9 0 10 0 10
set region half type 2
2000 settings made for type
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, 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) = 4.446 | 4.446 | 4.446 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms
Performance: 10758.705 tau/day, 24.904 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total---------------------------------------------------------------
Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75
Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95
Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13
Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00
Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14
Other | | 0.003027 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 85978 ave 85978 max 85978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 85978
Ave neighs/atom = 21.4945
Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
write_restart hybrid.restart
clear
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, 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) = 4.245 | 4.245 | 4.245 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms
Performance: 10713.932 tau/day, 24.801 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69
Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98
Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14
Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00
Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13
Other | | 0.004348 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5472 ave 5472 max 5472 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 86930 ave 86930 max 86930 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 86930
Ave neighs/atom = 21.7325
Neighbor list builds = 25
Dangerous builds = 25
clear
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data hybrid.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, 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) = 3.745 | 3.745 | 3.745 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms
Performance: 10868.626 tau/day, 25.159 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74
Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97
Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13
Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00
Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13
Other | | 0.002994 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5487 ave 5487 max 5487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 86831 ave 86831 max 86831 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 86831
Ave neighs/atom = 21.7078
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:00:30