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LAMMPS (29 Aug 2014)
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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 1 by 1 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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# 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 * * zbl 0.0 # Needed to activate hybrid cross-types
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pair_coeff 1 1 zbl ${zblz}
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pair_coeff 1 1 zbl 73
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pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
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SNAP Element = Ta, Radius 0.5, Weight 1
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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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Memory usage per processor = 2.92823 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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10 295.96579 -11.851053 0 -11.813095 2696.1559
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20 284.32535 -11.84956 0 -11.813095 2301.3713
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30 266.04602 -11.847215 0 -11.813095 1832.1745
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40 242.2862 -11.844168 0 -11.813095 1492.6765
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50 214.48968 -11.840603 0 -11.813094 1312.8908
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60 184.32523 -11.836734 0 -11.813094 1284.582
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70 153.58055 -11.832791 0 -11.813094 1374.4457
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80 124.04276 -11.829003 0 -11.813094 1537.703
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90 97.37622 -11.825582 0 -11.813094 1734.9662
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100 75.007873 -11.822714 0 -11.813094 1930.8005
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Loop time of 5.3587 on 1 procs for 100 steps with 128 atoms
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Pair time (%) = 5.35751 (99.9777)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000583649 (0.0108916)
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Outpt time (%) = 0.000120401 (0.00224684)
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Other time (%) = 0.000491381 (0.00916977)
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Nlocal: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 727 ave 727 max 727 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3712 ave 3712 max 3712 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 7424 ave 7424 max 7424 min
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Histogram: 1 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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@ -0,0 +1,116 @@
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LAMMPS (29 Aug 2014)
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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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# 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 * * zbl 0.0 # Needed to activate hybrid cross-types
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pair_coeff 1 1 zbl ${zblz}
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pair_coeff 1 1 zbl 73
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pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
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SNAP Element = Ta, Radius 0.5, Weight 1
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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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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 1.41452 on 4 procs for 100 steps with 128 atoms
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Pair time (%) = 1.36282 (96.3451)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.0507569 (3.58828)
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Outpt time (%) = 0.000217676 (0.0153887)
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Other time (%) = 0.000724733 (0.0512353)
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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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