git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3252 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/README

@@ -42,6 +42,7 @@ obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
 peri:	  Peridynamic model of cylinder impacted by indenter
 pour:     pouring of granular particles into a 3d box, then chute flow
+prd:      parallel replica dynamics of a vacancy diffusion in bulk Si
 reax:     RDX and TATB models using the ReaxFF
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void

examples/prd/in.prd

@@ -0,0 +1,95 @@
+# Parallel replica dynamics model for a single vacancy in bulk Si
+# events occur when a neighboring atom diffuses to the vacant site
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+
+# temperature
+
+variable t equal 1800.0
+
+# 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 $t 5287287 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 nvt $t $t 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             1000
+
+# output settings
+# only output atoms near vacancy
+
+compute coord all coord/atom $r
+dump events all custom 1 dump.events id type x y z
+dump_modify events thresh c_coord != 4
+
+restart  1 tmp.restart
+
+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         1 all event/displace 0.5
+
+prd  2000 100 10 10 100 1 54985 temp $t &
+     min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
+