forked from lijiext/lammps
63 lines
1.1 KiB
Plaintext
63 lines
1.1 KiB
Plaintext
|
# 2d NEB surface simulation, hop from surface to become adatom
|
||
|
|
|
||
|
|
dimension 2
|
||
|
|
boundary p s p
|
||
|
|
|
||
|
|
atom_style atomic
|
||
|
|
neighbor 0.3 bin
|
||
|
|
neigh_modify delay 5
|
||
|
|
atom_modify map array sort 0 0.0
|
||
|
|
|
||
|
|
variable u uloop 20
|
||
|
|
|
||
|
|
# create geometry with flat surface
|
||
|
|
|
||
|
|
lattice hex 0.9
|
||
|
|
region box block 0 20 0 10 -0.25 0.25
|
||
|
|
create_box 3 box
|
||
|
|
create_atoms 1 box
|
||
|
|
|
||
|
|
mass * 1.0
|
||
|
|
|
||
|
|
# LJ potentials
|
||
|
|
|
||
|
|
pair_style lj/cut 2.5
|
||
|
|
pair_coeff * * 1.0 1.0 2.5
|
||
|
|
|
||
|
|
# initial minimization to relax surface
|
||
|
|
|
||
|
|
minimize 1.0e-6 0.001 1000 10000
|
||
|
|
reset_timestep 0
|
||
|
|
|
||
|
|
# define groups
|
||
|
|
|
||
|
|
region 1 block INF INF INF 1.25 INF INF
|
||
|
|
group lower region 1
|
||
|
|
group mobile subtract all lower
|
||
|
|
set group lower type 2
|
||
|
|
|
||
|
|
timestep 0.005
|
||
|
|
|
||
|
|
# group of NEB atoms - either block or single atom ID 412
|
||
|
|
|
||
|
|
region surround block 10 18 17 20 0 0 units box
|
||
|
|
group one region surround
|
||
|
|
#group one id 412
|
||
|
|
set group one type 3
|
||
|
|
|
||
|
|
fix 1 lower setforce 0.0 0.0 0.0
|
||
|
|
fix 2 all neb 1.0
|
||
|
|
fix 3 all enforce2d
|
||
|
|
|
||
|
|
thermo 100
|
||
|
|
|
||
|
|
dump 1 all atom 10 tmp.dump.$u
|
||
|
|
dump_modify 1 scale no
|
||
|
|
|
||
|
|
# run NEB for 2000 steps or to force tolerance
|
||
|
|
|
||
|
|
min_style quickmin
|
||
|
|
|
||
|
|
#neb 0.0 1000 1000 100 final.hop1
|
||
|
|
neb 0.1 1000 1000 100 final.hop1
|