forked from lijiext/lammps
136 lines
4.2 KiB
Groff
136 lines
4.2 KiB
Groff
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LAMMPS (15 Feb 2016)
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# Demonstrate SNAP Ta potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.316
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice bcc $a
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lattice bcc 3.316
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Lattice spacing in x,y,z = 3.316 3.316 3.316
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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mass 1 180.88
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# choose potential
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include Ta06A_pot.snap
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# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
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# Definition of SNAP potential Ta_Cand06A
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# Assumes 1 LAMMPS atom type
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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# Specify hybrid with SNAP, ZBL
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pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 4.8 snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff 1 1 zbl 73 ${zblz}
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pair_coeff 1 1 zbl 73 73
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pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
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Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
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SNAP Element = Ta, Radius 0.5, Weight 1
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Reading potential file Ta06A.snapparam with DATE: 2014-09-05
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SNAP keyword rcutfac 4.67637
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SNAP keyword twojmax 6
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SNAP keyword gamma 1
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword diagonalstyle 3
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# Setup output
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459
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fix 1 all nve
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run ${nsteps}
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run 100
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.8
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ghost atom cutoff = 5.8
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binsize = 2.9 -> bins = 5 5 5
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Memory usage per processor = 2.91109 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -11.85157 0 -11.813095 2717.1661
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10 295.8664 -11.85104 0 -11.813095 2702.935
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20 283.95868 -11.849513 0 -11.813095 2301.3242
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30 265.29535 -11.847119 0 -11.813095 1870.3173
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40 241.09337 -11.844015 0 -11.813095 1568.1549
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50 212.86732 -11.840395 0 -11.813094 1409.2092
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60 182.35256 -11.836481 0 -11.813094 1389.0527
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70 151.38968 -11.83251 0 -11.813094 1474.9232
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80 121.80051 -11.828715 0 -11.813094 1627.6911
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90 95.262635 -11.825311 0 -11.813094 1812.9327
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100 73.194645 -11.822481 0 -11.813094 1995.2199
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Loop time of 0.899437 on 4 procs for 100 steps with 128 atoms
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Performance: 4.803 ns/day, 4.997 hours/ns, 111.181 timesteps/s
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99.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.87007 | 0.88069 | 0.8961 | 1.0 | 97.92
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0022893 | 0.017643 | 0.02821 | 7.2 | 1.96
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Output | 0.00027275 | 0.00029993 | 0.00037384 | 0.2 | 0.03
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Modify | 9.203e-05 | 0.00010943 | 0.0001235 | 0.1 | 0.01
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Other | | 0.0006917 | | | 0.08
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Nlocal: 32 ave 32 max 32 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 431 ave 431 max 431 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 928 ave 928 max 928 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 1856 ave 1856 max 1856 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7424
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Ave neighs/atom = 58
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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