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lammps/examples/python/log.4May2017.pair_python_melt.g++.4
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log.4May2017.pair_python_melt.g++.4
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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
# 3d Lennard-Jones melt
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 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 2.69 | 2.69 | 2.69 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 18.0035 on 4 procs for 250 steps with 4000 atoms
Performance: 5998.838 tau/day, 13.886 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.784 | 17.18 | 17.611 | 8.9 | 95.43
Neigh | 0.066257 | 0.066613 | 0.066967 | 0.1 | 0.37
Comm | 0.31192 | 0.74265 | 1.1386 | 42.7 | 4.13
Output | 0.000344 | 0.00076 | 0.001983 | 0.0 | 0.00
Modify | 0.010618 | 0.010763 | 0.010947 | 0.1 | 0.06
Other | | 0.00278 | | | 0.02
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
write_data melt.data
write_restart melt.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
4000 atoms
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 2.815 | 2.816 | 2.816 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 17.8516 on 4 procs for 250 steps with 4000 atoms
Performance: 6049.891 tau/day, 14.004 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.549 | 17.138 | 17.615 | 9.3 | 96.00
Neigh | 0.1326 | 0.13573 | 0.13709 | 0.5 | 0.76
Comm | 0.083467 | 0.56179 | 1.1533 | 51.4 | 3.15
Output | 0.000353 | 0.000703 | 0.00173 | 0.0 | 0.00
Modify | 0.011229 | 0.011437 | 0.011847 | 0.2 | 0.06
Other | | 0.004124 | | | 0.02
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2699 ave 2706 max 2693 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 37930.8 ave 39292 max 36264 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 151723
Ave neighs/atom = 37.9308
Neighbor list builds = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data melt.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 2.315 | 2.316 | 2.316 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 17.5277 on 4 procs for 250 steps with 4000 atoms
Performance: 6161.664 tau/day, 14.263 timesteps/s
31.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.46 | 17.032 | 17.348 | 8.3 | 97.17
Neigh | 0.063784 | 0.06495 | 0.065515 | 0.3 | 0.37
Comm | 0.10004 | 0.41613 | 0.98807 | 53.0 | 2.37
Output | 0.000331 | 0.00081525 | 0.002223 | 0.0 | 0.00
Modify | 0.010998 | 0.011169 | 0.011264 | 0.1 | 0.06
Other | | 0.002774 | | | 0.02
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 2695.5 ave 2706 max 2682 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 37927.2 ave 39002 max 36400 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 151709
Ave neighs/atom = 37.9273
Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:00:55
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