forked from lijiext/lammps
152 lines
5.1 KiB
Groff
152 lines
5.1 KiB
Groff
LAMMPS (15 Jun 2020)
|
|
# Demonstrate MLIAP interface to quadratic SNAP potential
|
|
|
|
# Initialize simulation
|
|
|
|
variable nsteps index 100
|
|
variable nrep equal 4
|
|
variable a equal 3.1803
|
|
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 3.1803
|
|
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
|
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 0.0 0.0) to (12.7212 12.7212 12.7212)
|
|
1 by 1 by 1 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 128 atoms
|
|
create_atoms CPU = 0.000 seconds
|
|
displace_atoms all random 0.01 0.01 0.01 12345
|
|
|
|
mass 1 183.84
|
|
|
|
# choose potential
|
|
|
|
include W.quadratic.mliap
|
|
# Definition of SNAP+ZBL potential.
|
|
variable zblcutinner equal 4
|
|
variable zblcutouter equal 4.8
|
|
variable zblz equal 74
|
|
|
|
# Specify hybrid with SNAP and ZBL
|
|
|
|
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
|
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
|
pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
|
SNAP keyword rcutfac 4.73442
|
|
SNAP keyword twojmax 6
|
|
SNAP keyword nelems 1
|
|
SNAP keyword elems W
|
|
SNAP keyword radelems 0.5
|
|
SNAP keyword welems 1
|
|
SNAP keyword rfac0 0.99363
|
|
SNAP keyword rmin0 0
|
|
SNAP keyword bzeroflag 1
|
|
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
|
pair_coeff 1 1 zbl 74 ${zblz}
|
|
pair_coeff 1 1 zbl 74 74
|
|
pair_coeff * * mliap W
|
|
|
|
|
|
# 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 no
|
|
|
|
# Run MD
|
|
|
|
velocity all create 300.0 4928459 loop geom
|
|
fix 1 all nve
|
|
run ${nsteps}
|
|
run 100
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check no
|
|
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 mliap, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 6.093 | 6.093 | 6.093 Mbytes
|
|
Step Temp E_pair c_energy TotEng Press v_press
|
|
0 300 -1.1602728 -1.1602728 -1.1217977 600047.3 -600047.3
|
|
10 288.46387 -1.1587932 -1.1587932 -1.1217976 600359.75 -600359.75
|
|
20 268.69718 -1.1562579 -1.1562579 -1.1217974 600870.22 -600870.22
|
|
30 243.19855 -1.1529874 -1.1529874 -1.1217971 601511.5 -601511.5
|
|
40 215.13122 -1.1493875 -1.1493875 -1.1217969 602202.36 -602202.36
|
|
50 187.82673 -1.1458855 -1.1458855 -1.1217966 602860.26 -602860.26
|
|
60 164.26822 -1.1428639 -1.1428639 -1.1217965 603413.25 -603413.25
|
|
70 146.65179 -1.1406045 -1.1406045 -1.1217964 603809.35 -603809.35
|
|
80 136.10769 -1.1392522 -1.1392522 -1.1217964 604022.32 -604022.32
|
|
90 132.62756 -1.138806 -1.138806 -1.1217964 604053.33 -604053.33
|
|
100 135.19841 -1.1391358 -1.1391358 -1.1217966 603928.48 -603928.48
|
|
Loop time of 1.69996 on 1 procs for 100 steps with 128 atoms
|
|
|
|
Performance: 2.541 ns/day, 9.444 hours/ns, 58.825 timesteps/s
|
|
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 1.6676 | 1.6676 | 1.6676 | 0.0 | 98.09
|
|
Neigh | 0.03029 | 0.03029 | 0.03029 | 0.0 | 1.78
|
|
Comm | 0.001238 | 0.001238 | 0.001238 | 0.0 | 0.07
|
|
Output | 0.000452 | 0.000452 | 0.000452 | 0.0 | 0.03
|
|
Modify | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.01
|
|
Other | | 0.000241 | | | 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 = 100
|
|
Dangerous builds not checked
|
|
|
|
Total wall time: 0:00:01
|