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in.tad
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# temperature accelerated dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperatures
variable tlo equal 1800.0
variable thi equal 2400.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a &
a1 1.0 0.0 0.0 &
a2 0.0 1.0 0.0 &
a3 0.0 0.0 1.0 &
basis 0.0 0.0 0.0 &
basis 0.0 0.5 0.5 &
basis 0.5 0.0 0.5 &
basis 0.5 0.5 0.0 &
basis 0.25 0.25 0.25 &
basis 0.25 0.75 0.75 &
basis 0.75 0.25 0.75 &
basis 0.75 0.75 0.25
region myreg block 0 4 &
0 4 &
0 4
create_box 1 myreg
create_atoms 1 region myreg
mass 1 28.06
group Si type 1
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
delete_atoms group del
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nve
fix 2 all langevin ${thi} ${thi} 0.1 48278
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 1000
# Eliminate COM motion
velocity all zero linear
# only output atoms near vacancy
compute coord all coord/atom $r
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute event all event/displace 1.0
unfix 1
unfix 2
fix 1 all nvt temp ${thi} ${thi} 0.1
# tad nsteps nevent tlo thi delta_conf tmax compute
# [min etol ftol niter neval]
# [neb etol_neb ftol_neb n1steps n2steps nevery]
# [min_style min_style]
# [neb_style min_style]
# [neb_log logfile]
tad 2000 50 ${tlo} ${thi} 0.05 1.0 event &
min ${etol} ${ftol} ${maxiter} ${maxeval} &
neb 0.0 0.01 200 200 20 &
min_style cg &
neb_style fire &
neb_log log.neb
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