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lammps/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
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log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
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LAMMPS (13 Feb 2017)
# Demonstrate SNAP Ta 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 2 box
Created orthogonal box = (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
mass 1 183.84
mass 2 4.0026
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
123 atoms in group tungsten
group helium type 2
5 atoms in group helium
# choose potential
include W.SNAP_HePair.pot
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
# 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 ...
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
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(2) pair snap, perpetual, skip from (6)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair table, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) pair table, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, half/full from (6)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(6) neighbor class addition, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 7.6729 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 290.48923 -10.436885 0 -10.399629 -5646.4813
20 271.18868 -10.434409 0 -10.399629 -5654.4646
30 246.2601 -10.431212 0 -10.399629 -5281.8873
40 218.69918 -10.427677 0 -10.399629 -4343.3636
50 189.12519 -10.423885 0 -10.399629 -2903.1138
60 155.55701 -10.419579 0 -10.399629 -1402.2278
70 118.83581 -10.414869 0 -10.399629 -146.36141
80 85.903126 -10.410645 0 -10.399628 857.74986
90 65.223651 -10.407993 0 -10.399628 1494.2746
100 59.833542 -10.407302 0 -10.399628 1938.9164
Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 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 | 11.072 | 11.072 | 11.072 | 0.0 | 99.99
Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00
Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00
Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00
Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00
Other | | 0.0003119 | | | 0.00
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: 3425 ave 3425 max 3425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6850 ave 6850 max 6850 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6850
Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:11
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