108 lines
3.7 KiB
Groff
108 lines
3.7 KiB
Groff
LAMMPS (10 Feb 2021)
|
|
# 3d Lennard-Jones melt
|
|
#
|
|
# This example requires that the example models provided with
|
|
# the kim-api package are installed. see the `./lib/kim/README` or
|
|
# `./lib/kim/Install.py` files for details on how to install these
|
|
# example models.
|
|
#
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
|
|
variable xx equal 20*$x
|
|
variable xx equal 20*1
|
|
variable yy equal 20*$y
|
|
variable yy equal 20*1
|
|
variable zz equal 20*$z
|
|
variable zz equal 20*1
|
|
|
|
kim init LennardJones_Ar real
|
|
#=== BEGIN kim init ==========================================
|
|
units real
|
|
neighbor 2.0 bin # Angstroms
|
|
timestep 1.0 # femtoseconds
|
|
|
|
This model has No mutable parameters.
|
|
#=== END kim init ============================================
|
|
|
|
|
|
lattice fcc 4.4300
|
|
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
|
|
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
|
region box block 0 20 0 ${yy} 0 ${zz}
|
|
region box block 0 20 0 20 0 ${zz}
|
|
region box block 0 20 0 20 0 20
|
|
create_box 1 box
|
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
|
|
1 by 1 by 1 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 32000 atoms
|
|
create_atoms CPU = 0.003 seconds
|
|
|
|
kim interactions Ar
|
|
#=== BEGIN kim interactions ==================================
|
|
pair_style kim LennardJones_Ar
|
|
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
|
|
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
|
|
pair_coeff * * Ar
|
|
#=== END kim interactions ====================================
|
|
|
|
|
|
mass 1 39.95
|
|
velocity all create 200.0 232345 loop geom
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 0 every 1 check yes
|
|
|
|
fix 1 all nve
|
|
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
|
|
|
run 100
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 8.45
|
|
ghost atom cutoff = 8.45
|
|
binsize = 4.225, bins = 21 21 21
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair kim, perpetual
|
|
attributes: full, newton off, cut 8.450000000000001
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 200 145069.63 0 164146.22 128015.94
|
|
100 95.179703 154939.42 0 164017.94 131602.75
|
|
Loop time of 2.8463 on 1 procs for 100 steps with 32000 atoms
|
|
|
|
Performance: 3.036 ns/day, 7.906 hours/ns, 35.133 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.5046 | 2.5046 | 2.5046 | 0.0 | 88.00
|
|
Neigh | 0.29437 | 0.29437 | 0.29437 | 0.0 | 10.34
|
|
Comm | 0.01182 | 0.01182 | 0.01182 | 0.0 | 0.42
|
|
Output | 7e-05 | 7e-05 | 7e-05 | 0.0 | 0.00
|
|
Modify | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.86
|
|
Other | | 0.01091 | | | 0.38
|
|
|
|
Nlocal: 32000.0 ave 32000 max 32000 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 19911.0 ave 19911 max 19911 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 4253750
|
|
Ave neighs/atom = 132.92969
|
|
Neighbor list builds = 3
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:02
|