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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 = 0.026 seconds
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
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
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
Creating table file spce.table with DATE: 2025-07-14
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
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
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
Reading pair table potential file spce.table with DATE: 2025-07-14
WARNING: 1 of 2000 force values in table OW-OW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:469)
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 table, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 37.03 | 37.03 | 37.03 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16690.019 0 -16690.019 -1268.9123
10 120.58553 -17767.489 0 -16689.521 -4063.8134
20 136.11736 -17882.538 0 -16665.724 -5124.6191
30 137.00764 -17872.301 0 -16647.528 -5337.1509
40 153.38867 -17999.256 0 -16628.046 -5213.5617
50 167.70342 -18103.046 0 -16603.87 -4460.622
60 163.07134 -18034.842 0 -16577.074 -3284.9619
70 169.59286 -18064.622 0 -16548.555 -2606.3637
80 182.92892 -18153.485 0 -16518.202 -2385.4748
90 191.27929 -18195.343 0 -16485.411 -2235.3292
100 194.68586 -18192.445 0 -16452.061 -1948.3379
Loop time of 2.57844 on 1 procs for 100 steps with 4500 atoms
Performance: 3.351 ns/day, 7.162 hours/ns, 38.783 timesteps/s, 174.524 katom-step/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 | 2.0568 | 2.0568 | 2.0568 | 0.0 | 79.77
Bond | 7.4804e-05 | 7.4804e-05 | 7.4804e-05 | 0.0 | 0.00
Kspace | 0.39621 | 0.39621 | 0.39621 | 0.0 | 15.37
Neigh | 0.092514 | 0.092514 | 0.092514 | 0.0 | 3.59
Comm | 0.0068884 | 0.0068884 | 0.0068884 | 0.0 | 0.27
Output | 0.00032237 | 0.00032237 | 0.00032237 | 0.0 | 0.01
Modify | 0.023601 | 0.023601 | 0.023601 | 0.0 | 0.92
Other | | 0.002014 | | | 0.08
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 = 2601768
Ave neighs/atom = 578.17067
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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