Added Si vacancy hop example

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11383 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/neb/README

@@ -2,6 +2,7 @@ Run these examples as:
 
 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

examples/neb/Si.sw

+# 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

examples/neb/final.sivac

+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 

examples/neb/in.neb.sivac

+# 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
+