From 29e25bd1267e08a7966b2e92dfbc9bedadd442a2 Mon Sep 17 00:00:00 2001
From: athomps <athomps@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 4 Jan 2011 23:35:26 +0000
Subject: [PATCH] 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 | 3 +-
examples/neb/in.neb.hop2 | 2 +-
examples/tad/README | 3 ++
examples/tad/Si.sw | 17 ++++++
examples/tad/in.tad | 113 +++++++++++++++++++++++++++++++++++++++
5 files changed, 135 insertions(+), 3 deletions(-)
create mode 100644 examples/tad/README
create mode 100644 examples/tad/Si.sw
create mode 100644 examples/tad/in.tad
diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1
index e7f0e96e27..d106d47a1a 100644
--- a/examples/neb/in.neb.hop1
+++ b/examples/neb/in.neb.hop1
@@ -60,5 +60,4 @@ dump 2 nonneb atom 10 dump.nonneb.$u
min_style quickmin
-#neb 0.0 1000 1000 100 final.hop1
-neb 0.1 1000 1000 100 final.hop1
+neb 0.0 0.1 1000 1000 100 final.hop1
diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2
index 4211299b6c..499d744afd 100644
--- a/examples/neb/in.neb.hop2
+++ b/examples/neb/in.neb.hop2
@@ -63,4 +63,4 @@ dump 2 nonneb atom 10 dump.nonneb.$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
diff --git a/examples/tad/README b/examples/tad/README
new file mode 100644
index 0000000000..1e17df6444
--- /dev/null
+++ b/examples/tad/README
@@ -0,0 +1,3 @@
+run this example as:
+
+mpirun -np 3 lmp_linux -partition 3x1 -in in.tad
diff --git a/examples/tad/Si.sw b/examples/tad/Si.sw
new file mode 100644
index 0000000000..16a56a2bc9
--- /dev/null
+++ b/examples/tad/Si.sw
@@ -0,0 +1,17 @@
+# 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
diff --git a/examples/tad/in.tad b/examples/tad/in.tad
new file mode 100644
index 0000000000..6c270a6ac3
--- /dev/null
+++ b/examples/tad/in.tad
@@ -0,0 +1,113 @@
+# 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
--
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