115 lines
3.8 KiB
Groff
115 lines
3.8 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# QTPIE Water
|
|
|
|
boundary p p p
|
|
units real
|
|
atom_style charge
|
|
|
|
read_data data.water
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
3000 atoms
|
|
read_data CPU = 0.008 seconds
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
|
|
replicate $x $y $z
|
|
replicate 1 $y $z
|
|
replicate 1 1 $z
|
|
replicate 1 1 1
|
|
Replication is creating a 1x1x1 = 1 times larger system...
|
|
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
|
1 by 2 by 2 MPI processor grid
|
|
3000 atoms
|
|
replicate CPU = 0.002 seconds
|
|
|
|
pair_style reaxff NULL safezone 3.0 mincap 150
|
|
pair_coeff * * qeq_ff.water O H
|
|
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
|
neighbor 0.5 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
velocity all create 300.0 4928459 rot yes dist gaussian
|
|
|
|
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
|
fix 2 all nvt temp 300 300 50.0
|
|
|
|
timestep 0.5
|
|
thermo 10
|
|
thermo_style custom step temp press density vol
|
|
|
|
run 20
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Your simulation uses code contributions which should be cited:
|
|
|
|
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
|
|
|
@Article{Aktulga12,
|
|
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
|
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
|
journal = {Parallel Computing},
|
|
year = 2012,
|
|
volume = 38,
|
|
number = {4--5},
|
|
pages = {245--259}
|
|
}
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 10.5
|
|
ghost atom cutoff = 10.5
|
|
binsize = 5.25, bins = 6 6 6
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair reaxff, perpetual
|
|
attributes: half, newton off, ghost
|
|
pair build: half/bin/ghost/newtoff
|
|
stencil: full/ghost/bin/3d
|
|
bin: standard
|
|
(2) fix qtpie/reaxff, perpetual, copy from (1)
|
|
attributes: half, newton off
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
|
Step Temp Press Density Volume
|
|
0 300 10138.375 1 29915.273
|
|
10 295.97879 3575.2769 1 29915.273
|
|
20 292.76583 10309.128 1 29915.273
|
|
Loop time of 1.53381 on 4 procs for 20 steps with 3000 atoms
|
|
|
|
Performance: 0.563 ns/day, 42.606 hours/ns, 13.039 timesteps/s, 39.118 katom-step/s
|
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.8105 | 0.82543 | 0.84031 | 1.4 | 53.82
|
|
Neigh | 0.041129 | 0.041436 | 0.041966 | 0.2 | 2.70
|
|
Comm | 0.0019875 | 0.016866 | 0.031795 | 9.9 | 1.10
|
|
Output | 3.2672e-05 | 3.6427e-05 | 4.734e-05 | 0.0 | 0.00
|
|
Modify | 0.64934 | 0.64987 | 0.65017 | 0.0 | 42.37
|
|
Other | | 0.0001691 | | | 0.01
|
|
|
|
Nlocal: 750 ave 760 max 735 min
|
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
|
Nghost: 6229.5 ave 6253 max 6191 min
|
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
|
Neighs: 277011 ave 280900 max 271380 min
|
|
Histogram: 1 0 0 0 1 0 0 0 1 1
|
|
|
|
Total # of neighbors = 1108044
|
|
Ave neighs/atom = 369.348
|
|
Neighbor list builds = 2
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:01
|