forked from lijiext/lammps
98 lines
2.3 KiB
Plaintext
98 lines
2.3 KiB
Plaintext
# Parallel replica 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 4 lmp_g++ -partition 4x1 -in in.prd
|
|
|
|
#log none
|
|
|
|
units metal
|
|
|
|
atom_style atomic
|
|
atom_modify map array
|
|
boundary p p p
|
|
atom_modify sort 0 0.0
|
|
|
|
# temperature
|
|
|
|
variable t equal 1800.0
|
|
|
|
# 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 $t 5287287 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 nvt temp $t $t 0.1
|
|
|
|
timestep 1.0e-3
|
|
neighbor 1.0 bin
|
|
neigh_modify every 1 delay 10 check yes
|
|
|
|
# equilibrate
|
|
|
|
run 100
|
|
|
|
# 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 1 all event/displace 0.5
|
|
|
|
prd 2000 100 10 10 100 1 54985 temp $t &
|
|
min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|