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lammps/examples/python/log.4May17.pair_python_long.g++.4
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log.4May17.pair_python_long.g++.4
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LAMMPS (4 May 2017)
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 python 12.0
pair_coeff * * py_pot.LJCutSPCE OW HW
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
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
# switch to tabulated potential with long-range coulomb as overlay
pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 1 table spce.table OW-OW
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 coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair table, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16690.032 0 -16690.032 -1268.9538
10 120.58553 -17767.504 0 -16689.536 -4063.8589
20 136.11736 -17882.557 0 -16665.742 -5124.6758
30 137.00764 -17872.318 0 -16647.545 -5337.2022
40 153.38868 -17999.269 0 -16628.059 -5213.6001
50 167.70342 -18103.06 0 -16603.883 -4460.6632
60 163.07134 -18034.856 0 -16577.088 -3285.0037
70 169.59286 -18064.636 0 -16548.57 -2606.407
80 182.92893 -18153.499 0 -16518.215 -2385.5152
90 191.2793 -18195.356 0 -16485.425 -2235.3701
100 194.68587 -18192.458 0 -16452.073 -1948.3746
Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms
Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 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 | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49
Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01
Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86
Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83
Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68
Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02
Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95
Other | | 0.003775 | | | 0.16
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: 650442 ave 678831 max 626373 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 2601769
Ave neighs/atom = 578.171
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:02
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