2010-10-01 07:12:46 +08:00
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# 2d NEB surface simulation, hop from surface to become adatom
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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variable u uloop 20
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# create geometry with flat surface
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lattice hex 0.9
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region box block 0 20 0 10 -0.25 0.25
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create_box 3 box
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create_atoms 1 box
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mass * 1.0
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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2010-10-23 05:24:52 +08:00
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pair_modify shift yes
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2010-10-01 07:12:46 +08:00
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# initial minimization to relax surface
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2010-10-07 07:33:17 +08:00
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minimize 1.0e-6 1.0e-4 1000 10000
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2010-10-01 07:12:46 +08:00
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reset_timestep 0
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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2014-01-31 05:11:09 +08:00
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timestep 0.05
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2010-10-01 07:12:46 +08:00
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# group of NEB atoms - either block or single atom ID 412
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region surround block 10 18 17 20 0 0 units box
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2010-10-07 07:33:17 +08:00
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group nebatoms region surround
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#group nebatoms id 412
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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2010-10-01 07:12:46 +08:00
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fix 1 lower setforce 0.0 0.0 0.0
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2010-10-07 07:33:17 +08:00
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fix 2 nebatoms neb 1.0
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2010-10-01 07:12:46 +08:00
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fix 3 all enforce2d
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thermo 100
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2012-01-13 03:03:12 +08:00
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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2010-10-01 07:12:46 +08:00
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# run NEB for 2000 steps or to force tolerance
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min_style quickmin
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2014-01-11 04:49:34 +08:00
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neb 0.0 0.1 1000 1000 100 final final.hop1
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