LAMMPS (4 May 2017)
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 * * py_pot.LJCutMelt lj
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
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
pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
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 table, 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 -6.7733629 0 -2.2744879 -3.7032813
50 1.675395 -4.7945736 0 -2.2821094 5.6620623
100 1.6503067 -4.7558145 0 -2.2809733 5.8055967
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
200 1.6371471 -4.7363942 0 -2.2812874 5.924977
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms
Performance: 370058.286 tau/day, 856.616 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06
Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96
Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30
Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05
Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22
Other | | 0.001211 | | | 0.42
Nlocal: 1000 ave 1010 max 981 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703 ave 2715 max 2688 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 37915.2 ave 39191 max 36151 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 151661
Ave neighs/atom = 37.9153
Neighbor list builds = 12
Dangerous builds not checked
shell rm lj_1_1.table
Total wall time: 0:00:00