New example folder for fire

These examples are similar to those in the "min" and "neb" folders.

Each example can be run with the following minimization style:

- quickmin:                             qm

- fire:  	                        fire

- fire with optimized options:          fire_mod

- fire with min_modify options to

  reproduce fire/old:                   fire_mod_old

- fire/old (previous implementation):   fire_old

Run the NEB examples as:

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.qm

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod_old

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_old

mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.qm

mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire

mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod

mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod_old

mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_old

# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber,  Phys Rev B, 31, 5262, (1985)

# 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 

# 2d Lennard-Jones melt and subsequent energy minimization

units		lj

dimension	2

atom_style	atomic

lattice		sq2 0.8442

region		box block 0 20 0 20 -0.1 0.1

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 5.0 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

pair_modify	shift yes

neighbor	0.3 bin

neigh_modify	delay 0 every 1 check yes

fix		1 all nve

fix		2 all enforce2d

#dump		1 all atom 100 dump.min

#dump		2 all image 50 image.*.jpg type type &

#		zoom 1.6 adiam 1.5

#dump_modify	2 pad 4

#dump		3 all movie 50 movie.mpg type type &

#		zoom 1.6 adiam 1.5

#dump_modify	3 pad 4

thermo		100

run		1000

neigh_modify	delay 0 every 1 check yes

#dump_modify	1 every 25

thermo		50

min_style	cg

minimize	0.0 1.0e-6 10000 10000

# 2d Lennard-Jones melt and subsequent energy minimization

units		lj

dimension	2

atom_style	atomic

lattice		sq2 0.8442

region		box block 0 20 0 20 -0.1 0.1

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 5.0 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

pair_modify	shift yes

neighbor	0.3 bin

neigh_modify	delay 0 every 1 check yes

fix		1 all nve

fix		2 all enforce2d

#dump		1 all atom 100 dump.min

#dump		2 all image 50 image.*.jpg type type &

#		zoom 1.6 adiam 1.5

#dump_modify	2 pad 4

#dump		3 all movie 50 movie.mpg type type &

#		zoom 1.6 adiam 1.5

#dump_modify	3 pad 4

thermo		100

run		1000

neigh_modify	delay 0 every 1 check yes

#dump_modify	1 every 25

thermo		50

min_style	fire

minimize	0.0 1.0e-6 10000 10000