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lammps/examples/python/log.4May17.pair_python_coulomb.g++.1
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log.4May17.pair_python_coulomb.g++.1
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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)
1 by 1 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 hybrid/overlay coul/long 12.0 python 12.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
pair_modify table 0
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 combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
PPPM initialization ...
WARNING: Using polynomial approximation 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 = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
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 python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation 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 = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation 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 = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
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 = 103823 64000
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 table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -100272.97 0 -100272.97 -1282.0708
10 120.61568 -101350.63 0 -100272.39 -4077.5051
20 136.11379 -101465.43 0 -100248.65 -5136.5677
30 137.01602 -101455.3 0 -100230.46 -5347.8311
40 153.424 -101582.46 0 -100210.93 -5223.1676
50 167.73654 -101686.24 0 -100186.77 -4468.6687
60 163.11642 -101618.16 0 -100159.99 -3291.7815
70 169.64512 -101647.89 0 -100131.35 -2611.638
80 182.9979 -101737.01 0 -100101.11 -2390.6293
90 191.33873 -101778.71 0 -100068.24 -2239.386
100 194.7458 -101775.84 0 -100034.92 -1951.9128
Loop time of 7.63869 on 1 procs for 100 steps with 4500 atoms
Performance: 1.131 ns/day, 21.219 hours/ns, 13.091 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7777 | 5.7777 | 5.7777 | 0.0 | 75.64
Bond | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00
Kspace | 1.5385 | 1.5385 | 1.5385 | 0.0 | 20.14
Neigh | 0.22962 | 0.22962 | 0.22962 | 0.0 | 3.01
Comm | 0.024123 | 0.024123 | 0.024123 | 0.0 | 0.32
Output | 0.00061131 | 0.00061131 | 0.00061131 | 0.0 | 0.01
Modify | 0.062444 | 0.062444 | 0.062444 | 0.0 | 0.82
Other | | 0.005466 | | | 0.07
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21216 ave 21216 max 21216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601766
Ave neighs/atom = 578.17
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:07
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