Added tad example

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5473 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/neb/in.neb.hop1

@@ -60,5 +60,4 @@ dump		2 nonneb atom 10 dump.nonneb.$u
 
 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

examples/neb/in.neb.hop2

@@ -63,4 +63,4 @@ dump		2 nonneb atom 10 dump.nonneb.$u
 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

examples/tad/README

+run this example as:
+
+mpirun -np 3 lmp_linux -partition 3x1 -in in.tad

examples/tad/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/tad/in.tad

+# 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