Added tad example

min_style	quickmin

#neb		0.0 1000 1000 100 final.hop1

neb		0.1 1000 1000 100 final.hop1

neb		0.0 0.1 1000 1000 100 final.hop1

min_style	fire

#neb		0.0 1000 1000 100 final.hop2

neb		0.01 1000 1000 100 final.hop2

neb		0.0 0.01 1000 1000 100 final.hop2

run this example as:

mpirun -np 3 lmp_linux -partition 3x1 -in in.tad

# Stillinger-Weber parameters for various elements and mixtures

# multiple entries can be added to this file, LAMMPS reads the ones it needs

# these entries are in LAMMPS "metal" units:

#   epsilon = eV; sigma = Angstroms

#   other quantities are unitless

# format of a single entry (one or more lines):

#   element 1, element 2, element 3, 

#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol

# Here are the original parameters in metal units, for Silicon from:

#

# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)

#

Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333

         7.049556277  0.6022245584  4.0  0.0 0.0

# 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