forked from lijiext/lammps
155 lines
5.1 KiB
Plaintext
155 lines
5.1 KiB
Plaintext
LAMMPS (19 Mar 2020)
|
|
# 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
|
|
create_atoms CPU = 0.000254 secs
|
|
|
|
mass 1 180.88
|
|
|
|
# choose potential
|
|
|
|
include Ta06A.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 zbl ${zblcutinner} ${zblcutouter} snap
|
|
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
|
|
pair_style hybrid/overlay zbl 4 4.8 snap
|
|
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 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 rfac0 0.99363
|
|
SNAP keyword rmin0 0
|
|
SNAP keyword bzeroflag 0
|
|
SNAP keyword quadraticflag 0
|
|
|
|
|
|
# Setup output
|
|
|
|
compute eatom all pe/atom
|
|
compute energy all reduce sum c_eatom
|
|
|
|
compute satom all stress/atom NULL
|
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
|
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
|
|
|
thermo_style custom step temp epair c_energy etotal press v_press
|
|
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 ...
|
|
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
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair zbl, perpetual, half/full from (2)
|
|
attributes: half, newton on
|
|
pair build: halffull/newton
|
|
stencil: none
|
|
bin: none
|
|
(2) pair snap, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes
|
|
Step Temp E_pair c_energy TotEng Press v_press
|
|
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
|
10 295.96579 -11.851053 -11.851053 -11.813095 2696.1559 -2696.1559
|
|
20 284.32535 -11.84956 -11.84956 -11.813095 2301.3713 -2301.3713
|
|
30 266.04602 -11.847215 -11.847215 -11.813095 1832.1745 -1832.1745
|
|
40 242.2862 -11.844168 -11.844168 -11.813095 1492.6765 -1492.6765
|
|
50 214.48968 -11.840603 -11.840603 -11.813094 1312.8908 -1312.8908
|
|
60 184.32523 -11.836734 -11.836734 -11.813094 1284.582 -1284.582
|
|
70 153.58055 -11.832791 -11.832791 -11.813094 1374.4457 -1374.4457
|
|
80 124.04276 -11.829003 -11.829003 -11.813094 1537.703 -1537.703
|
|
90 97.37622 -11.825582 -11.825582 -11.813094 1734.9662 -1734.9662
|
|
100 75.007873 -11.822714 -11.822714 -11.813094 1930.8005 -1930.8005
|
|
Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms
|
|
|
|
Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s
|
|
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.99426 | 0.99426 | 0.99426 | 0.0 | 99.89
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.000305 | 0.000305 | 0.000305 | 0.0 | 0.03
|
|
Output | 0.000413 | 0.000413 | 0.000413 | 0.0 | 0.04
|
|
Modify | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.02
|
|
Other | | 0.000191 | | | 0.02
|
|
|
|
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: 0:00:01
|