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Run these examples as:
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mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1
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mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2
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Create dump files to do visualization from as:
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(see lammps/tools/README for more info on these Python scripts)
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python ~/lammps/tools/python/neb1.py dump.hop1.a 3 tmp.dump.*
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python ~/lammps/tools/python/neb2.py dump.hop1.b tmp.dump.*
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dump.hop1.a = series of snapshots for all replicas together
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time = progression of NEB calculation
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dump.hop1.b = series of snapshots for final state of all replicas
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time = replica #
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412 14.0 20.5 0
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421 14.0 20.5 0
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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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# initial minimization to relax surface
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minimize 1.0e-6 0.001 1000 10000
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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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timestep 0.005
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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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group one region surround
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#group one id 412
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set group one type 3
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 all neb 1.0
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fix 3 all enforce2d
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thermo 100
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dump 1 all atom 10 tmp.dump.$u
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dump_modify 1 scale no
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# run NEB for 2000 steps or to force tolerance
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min_style quickmin
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#neb 0.0 1000 1000 100 final.hop1
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neb 0.1 1000 1000 100 final.hop1
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# 2d NEB surface simulation, hop of adatom on surface
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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 adatom
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lattice hex 0.9
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region box block 0 20 0 11 -0.25 0.25
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region box1 block 0 20 0 10 -0.25 0.25
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create_box 3 box
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create_atoms 1 region box1
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create_atoms 1 single 11.5 10.5 0
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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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# initial minimization to relax surface
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minimize 1.0e-6 0.001 1000 10000
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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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timestep 0.005
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# group of NEB atoms - either block or single atom ID 421
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region surround block 10 18 17 21 0 0 units box
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group one region surround
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#group one id 421
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set group one type 3
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 one neb 1.0
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fix 3 all enforce2d
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thermo 10
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dump 1 all atom 10 tmp.dump.$u
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dump_modify 1 scale no
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# run NEB for 2000 steps or to force tolerance
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min_style fire
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#neb 0.0 1000 1000 100 final.hop2
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neb 0.01 1000 1000 100 final.hop2
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LAMMPS (29 Sep 2010)
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Running on 4 partitions of processors
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Step RD1 PE1 RD2 PE2 ... RDN PEN
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0 0 -3.19266 0.333333 -2.75656 0.666667 -2.88382 1 -3.18641
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100 0 -3.19267 0.325226 -3.18617 0.627987 -3.18537 1 -3.18765
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175 0 -3.19267 0.321396 -3.18621 0.644098 -3.18536 1 -3.18766
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Step RD1 PE1 RD2 PE2 ... RDN PEN
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175 0 -3.19267 0.321396 -3.18621 0.644098 -3.18536 1 -3.18766
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275 0 -3.19267 0.321136 -3.18621 0.633855 -3.18535 1 -3.18766
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345 0 -3.19268 0.318221 -3.18625 0.617506 -3.18538 1 -3.18766
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LAMMPS (29 Sep 2010)
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Running on 4 partitions of processors
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Step RD1 PE1 RD2 PE2 ... RDN PEN
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0 0 -3.19051 0.333333 -3.18866 0.666667 -3.18862 1 -3.18934
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100 0 -3.19051 0.293005 -3.18936 0.59723 -3.18895 1 -3.19051
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200 0 -3.19052 0.300372 -3.18932 0.633185 -3.18904 1 -3.19051
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300 0 -3.19052 0.315043 -3.18926 0.644819 -3.18908 1 -3.19052
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400 0 -3.19052 0.323255 -3.18923 0.655365 -3.18911 1 -3.19052
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500 0 -3.19052 0.326135 -3.18922 0.658828 -3.18913 1 -3.19052
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600 0 -3.19052 0.328852 -3.18921 0.662529 -3.18914 1 -3.19052
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700 0 -3.19052 0.330378 -3.1892 0.664116 -3.18918 1 -3.19052
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763 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052
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Step RD1 PE1 RD2 PE2 ... RDN PEN
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763 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052
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863 0 -3.19052 0.278536 -3.18942 0.502167 -3.18884 1 -3.19052
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963 0 -3.19052 0.260586 -3.18952 0.503636 -3.18884 1 -3.19052
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1049 0 -3.19052 0.254838 -3.18955 0.504648 -3.18884 1 -3.19052
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