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lammps/examples/snap/log.5Oct16.snap.g++.1
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LAMMPS (5 Oct 2016)
# Demonstrate SNAP Ta potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.316
Lattice spacing in x,y,z = 3.316 3.316 3.316
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
mass 1 180.88
# choose potential
include Ta06A_pot.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 4.8
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.8
ghost atom cutoff = 5.8
binsize = 2.9 -> bins = 5 5 5
Memory usage per processor = 2.92823 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.96579 -11.851053 0 -11.813095 2696.1559
20 284.32535 -11.84956 0 -11.813095 2301.3713
30 266.04602 -11.847215 0 -11.813095 1832.1745
40 242.2862 -11.844168 0 -11.813095 1492.6765
50 214.48968 -11.840603 0 -11.813094 1312.8908
60 184.32523 -11.836734 0 -11.813094 1284.582
70 153.58055 -11.832791 0 -11.813094 1374.4457
80 124.04276 -11.829003 0 -11.813094 1537.703
90 97.37622 -11.825582 0 -11.813094 1734.9662
100 75.007873 -11.822714 0 -11.813094 1930.8005
Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms
Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 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 | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01
Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00
Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01
Other | | 0.0002978 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3712 ave 3712 max 3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7424 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
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