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