From c42f8c43f5bb2375e9802d588f877785205e698f Mon Sep 17 00:00:00 2001 From: athomps <athomps@f3b2605a-c512-4ea7-a41b-209d697bcdaa> Date: Wed, 29 Jan 2014 22:51:52 +0000 Subject: [PATCH] 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 | 1 + examples/neb/Si.sw | 17 +++++++++ examples/neb/final.sivac | 8 +++++ examples/neb/in.neb.sivac | 76 +++++++++++++++++++++++++++++++++++++++ 4 files changed, 102 insertions(+) create mode 100644 examples/neb/Si.sw create mode 100644 examples/neb/final.sivac create mode 100644 examples/neb/in.neb.sivac diff --git a/examples/neb/README b/examples/neb/README index c512726727..137c42a068 100644 --- a/examples/neb/README +++ b/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 diff --git a/examples/neb/Si.sw b/examples/neb/Si.sw new file mode 100644 index 0000000000..16a56a2bc9 --- /dev/null +++ b/examples/neb/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/neb/final.sivac b/examples/neb/final.sivac new file mode 100644 index 0000000000..a0e2a2ed60 --- /dev/null +++ b/examples/neb/final.sivac @@ -0,0 +1,8 @@ +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 diff --git a/examples/neb/in.neb.sivac b/examples/neb/in.neb.sivac new file mode 100644 index 0000000000..baf87bf215 --- /dev/null +++ b/examples/neb/in.neb.sivac @@ -0,0 +1,76 @@ +# 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 + -- GitLab