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LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
read_data data.spce
Reading data file ...
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
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading bonds ...
3000 bonds
reading angles ...
1500 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.015 seconds
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
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
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
1500 = # of frozen angles
find clusters CPU = 0.001 seconds
fix 2 all nvt temp 300.0 300.0 100.0
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb
G vector (1/distance) = 0.27965195
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394674
estimated relative force accuracy = 1.188549e-06
using double precision FFTW3
3d grid and FFT values/proc = 103823 64000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 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
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 41.61 | 41.61 | 41.61 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.368 0 -16692.368 -1289.2219
10 120.56861 -17769.718 0 -16691.901 -4082.7095
20 136.08014 -17884.591 0 -16668.109 -5140.7821
30 136.97316 -17874.351 0 -16649.886 -5351.3565
40 153.37285 -18001.492 0 -16630.424 -5227.06
50 167.70413 -18105.435 0 -16606.252 -4473.209
60 163.08253 -18037.29 0 -16579.422 -3295.8958
70 169.60395 -18067.078 0 -16550.912 -2615.7023
80 182.94811 -18155.978 0 -16520.523 -2393.3158
90 191.29902 -18197.887 0 -16487.779 -2242.7102
100 194.70949 -18195.02 0 -16454.425 -1955.2914
Loop time of 5.76164 on 1 procs for 100 steps with 4500 atoms
Performance: 1.500 ns/day, 16.005 hours/ns, 17.356 timesteps/s, 78.103 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2241 | 5.2241 | 5.2241 | 0.0 | 90.67
Bond | 8.2871e-05 | 8.2871e-05 | 8.2871e-05 | 0.0 | 0.00
Kspace | 0.40456 | 0.40456 | 0.40456 | 0.0 | 7.02
Neigh | 0.099403 | 0.099403 | 0.099403 | 0.0 | 1.73
Comm | 0.0071032 | 0.0071032 | 0.0071032 | 0.0 | 0.12
Output | 0.00030889 | 0.00030889 | 0.00030889 | 0.0 | 0.01
Modify | 0.023994 | 0.023994 | 0.023994 | 0.0 | 0.42
Other | | 0.002088 | | | 0.04
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: 2.60176e+06 ave 2.60176e+06 max 2.60176e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601762
Ave neighs/atom = 578.16933
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:05
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