Added Si vacancy hop example

mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1

mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2

mpirun -np 3 lmp_linux -partition 3x1 -in in.neb.sivac

Create dump files to do visualization from via Python tools:

(see lammps/tools/README and lammps/tools/python/README

# 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

7

174  6.86775 9.49992 9.62069 

175  9.46441 6.90709 9.62317 

301  6.87004 6.90631 12.2171 

304  8.44266 8.48312 11.1965 

306  10.5121 8.48457 13.2624 

331  8.44223 10.5435 13.2633 

337  10.5124 10.5437 11.1959 

# NEB simulation of vacancy hopping in silicon crystal

units           metal

atom_style      atomic

atom_modify     map array

boundary        p p p

atom_modify	sort 0 0.0

# coordination number cutoff

variable r equal 2.835

# 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

# make a vacancy

group del id 300

delete_atoms group del

group vacneigh id 174 175 301 304 306 331 337

# choose potential

pair_style      sw

pair_coeff * * Si.sw Si

# set up neb run

variable	u uloop 20

# only output atoms near vacancy

dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z

# initial minimization to relax vacancy

displace_atoms all random 0.1 0.1 0.1 123456

minimize	1.0e-6 1.0e-4 1000 10000

reset_timestep	0

fix		1 all neb 1.0

thermo		100

# run NEB for 2000 steps or to force tolerance

timestep        0.01

min_style	quickmin

neb		0.0 0.01 50 100 10 final final.sivac