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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12426 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-09-05 23:24:15 +00:00
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commit 3e4d6f2096
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LAMMPS (29 Aug 2014)
# 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
# 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 * * zbl 0.0 # Needed to activate hybrid cross-types
pair_coeff 1 1 zbl ${zblz}
pair_coeff 1 1 zbl 73
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
SNAP Element = Ta, Radius 0.5, Weight 1
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
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 5.3587 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 5.35751 (99.9777)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000583649 (0.0108916)
Outpt time (%) = 0.000120401 (0.00224684)
Other time (%) = 0.000491381 (0.00916977)
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

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LAMMPS (29 Aug 2014)
# 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 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
mass 1 180.88
# choose potential
include Ta06A_pot.snap
# 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 * * zbl 0.0 # Needed to activate hybrid cross-types
pair_coeff 1 1 zbl ${zblz}
pair_coeff 1 1 zbl 73
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
SNAP Element = Ta, Radius 0.5, Weight 1
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
Memory usage per processor = 2.91109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.8664 -11.85104 0 -11.813095 2702.935
20 283.95868 -11.849513 0 -11.813095 2301.3242
30 265.29535 -11.847119 0 -11.813095 1870.3173
40 241.09337 -11.844015 0 -11.813095 1568.1549
50 212.86732 -11.840395 0 -11.813094 1409.2092
60 182.35256 -11.836481 0 -11.813094 1389.0527
70 151.38968 -11.83251 0 -11.813094 1474.9232
80 121.80051 -11.828715 0 -11.813094 1627.6911
90 95.262635 -11.825311 0 -11.813094 1812.9327
100 73.194645 -11.822481 0 -11.813094 1995.2199
Loop time of 1.41452 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 1.36282 (96.3451)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0507569 (3.58828)
Outpt time (%) = 0.000217676 (0.0153887)
Other time (%) = 0.000724733 (0.0512353)
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1856 ave 1856 max 1856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0