diff --git a/examples/README b/examples/README index d89f87308a..71580906f9 100644 --- a/examples/README +++ b/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 diff --git a/examples/prd/in.prd b/examples/prd/in.prd new file mode 100644 index 0000000000..3f6e21605f --- /dev/null +++ b/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 +