diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 index f26b52a28a..54a22a5b87 100644 --- a/examples/neb/in.neb.hop1 +++ b/examples/neb/in.neb.hop1 @@ -1,66 +1,66 @@ # 2d NEB surface simulation, hop from surface to become adatom -dimension 2 -boundary p s p +dimension 2 +boundary p s p -atom_style atomic -neighbor 0.3 bin -neigh_modify delay 5 -atom_modify map array sort 0 0.0 +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 -variable u uloop 20 +variable u uloop 20 # create geometry with flat surface -lattice hex 0.9 -region box block 0 20 0 10 -0.25 0.25 +lattice hex 0.9 +region box block 0 20 0 10 -0.25 0.25 -#create_box 3 box -#create_atoms 1 box -#mass * 1.0 +#create_box 3 box +#create_atoms 1 box +#mass * 1.0 #write_data initial.hop1 read_data initial.hop1 # LJ potentials -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 -pair_modify shift yes +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_modify shift yes # initial minimization to relax surface -minimize 1.0e-6 1.0e-4 1000 10000 -reset_timestep 0 +minimize 1.0e-6 1.0e-4 1000 10000 +reset_timestep 0 # define groups -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -group mobile subtract all lower -set group lower type 2 +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 -timestep 0.05 +timestep 0.05 # group of NEB atoms - either block or single atom ID 412 -region surround block 10 18 17 20 0 0 units box -group nebatoms region surround -#group nebatoms id 412 -set group nebatoms type 3 -group nonneb subtract all nebatoms +region surround block 10 18 17 20 0 0 units box +group nebatoms region surround +#group nebatoms id 412 +set group nebatoms type 3 +group nonneb subtract all nebatoms -fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 parallel ideal -fix 3 all enforce2d +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 nebatoms neb 1.0 parallel ideal +fix 3 all enforce2d -thermo 100 +thermo 100 -#dump 1 nebatoms atom 10 dump.neb.$u -#dump 2 nonneb atom 10 dump.nonneb.$u +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance -min_style quickmin +min_style quickmin -neb 0.0 0.1 1000 1000 100 final final.hop1 +neb 0.0 0.1 1000 1000 100 final final.hop1 diff --git a/examples/neb/in.neb.hop1.end b/examples/neb/in.neb.hop1.end index 81e5315306..c5e08b40f1 100644 --- a/examples/neb/in.neb.hop1.end +++ b/examples/neb/in.neb.hop1.end @@ -1,56 +1,56 @@ # 2d NEB surface simulation, hop from surface to become adatom -dimension 2 -boundary p s p +dimension 2 +boundary p s p -atom_style atomic -neighbor 0.3 bin -neigh_modify delay 5 -atom_modify map array sort 0 0.0 +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 -variable u uloop 20 +variable u uloop 20 # create geometry with flat surface -lattice hex 0.9 -region box block 0 20 0 10 -0.25 0.25 +lattice hex 0.9 +region box block 0 20 0 10 -0.25 0.25 read_data initial.hop1.end # LJ potentials -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 -pair_modify shift yes +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_modify shift yes # define groups -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -group mobile subtract all lower -set group lower type 2 +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 -timestep 0.05 +timestep 0.05 # group of NEB atoms - either block or single atom ID 412 -region surround block 10 18 17 20 0 0 units box -group nebatoms region surround -#group nebatoms id 412 -set group nebatoms type 3 -group nonneb subtract all nebatoms +region surround block 10 18 17 20 0 0 units box +group nebatoms region surround +#group nebatoms id 412 +set group nebatoms type 3 +group nonneb subtract all nebatoms -fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 parallel ideal end first 1.0 -fix 3 all enforce2d +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 nebatoms neb 1.0 parallel ideal end first 1.0 +fix 3 all enforce2d -thermo 100 +thermo 100 -#dump 1 nebatoms atom 10 dump.neb.$u -#dump 2 nonneb atom 10 dump.nonneb.$u +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance -min_style quickmin +min_style quickmin -neb 0.0 0.1 1000 1000 100 final final.hop1 +neb 0.0 0.1 1000 1000 100 final final.hop1 diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 index e69fb338cd..97512dbbf9 100644 --- a/examples/neb/in.neb.hop2 +++ b/examples/neb/in.neb.hop2 @@ -1,68 +1,68 @@ # 2d NEB surface simulation, hop of adatom on surface -dimension 2 -boundary p s p +dimension 2 +boundary p s p -atom_style atomic -neighbor 0.3 bin -neigh_modify delay 5 -atom_modify map array sort 0 0.0 +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 -variable u uloop 20 +variable u uloop 20 # create geometry with adatom -lattice hex 0.9 -region box block 0 20 0 11 -0.25 0.25 -region box1 block 0 20 0 10 -0.25 0.25 +lattice hex 0.9 +region box block 0 20 0 11 -0.25 0.25 +region box1 block 0 20 0 10 -0.25 0.25 -#create_box 3 box -#create_atoms 1 region box1 -#create_atoms 1 single 11.5 10.5 0 -#mass * 1.0 +#create_box 3 box +#create_atoms 1 region box1 +#create_atoms 1 single 11.5 10.5 0 +#mass * 1.0 #write_data initial.hop2 read_data initial.hop2 # LJ potentials -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 -pair_modify shift yes +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_modify shift yes # initial minimization to relax surface -minimize 1.0e-6 1.0e-4 1000 10000 -reset_timestep 0 +minimize 1.0e-6 1.0e-4 1000 10000 +reset_timestep 0 # define groups -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -group mobile subtract all lower -set group lower type 2 +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 -timestep 0.05 +timestep 0.05 # group of NEB atoms - either block or single atom ID 421 -region surround block 10 18 17 21 0 0 units box -group nebatoms region surround -#group nebatoms id 421 -set group nebatoms type 3 -group nonneb subtract all nebatoms +region surround block 10 18 17 21 0 0 units box +group nebatoms region surround +#group nebatoms id 421 +set group nebatoms type 3 +group nonneb subtract all nebatoms -fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 -fix 3 all enforce2d +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 nebatoms neb 1.0 +fix 3 all enforce2d -thermo 100 +thermo 100 -#dump 1 nebatoms atom 10 dump.neb.$u -#dump 2 nonneb atom 10 dump.nonneb.$u +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance -min_style fire +min_style fire -neb 0.0 0.05 1000 1000 100 final final.hop2 +neb 0.0 0.05 1000 1000 100 final final.hop2 diff --git a/examples/neb/in.neb.sivac b/examples/neb/in.neb.sivac index 7a35174466..22492328c6 100644 --- a/examples/neb/in.neb.sivac +++ b/examples/neb/in.neb.sivac @@ -5,7 +5,7 @@ units metal atom_style atomic atom_modify map array boundary p p p -atom_modify sort 0 0.0 +atom_modify sort 0 0.0 # coordination number cutoff @@ -45,7 +45,7 @@ group Si type 1 group del id 300 delete_atoms group del compress no group vacneigh id 174 175 301 304 306 331 337 - + # choose potential pair_style sw @@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si # set up neb run -variable u uloop 20 - -# only output atoms near vacancy - +variable u uloop 20 # 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 +minimize 1.0e-6 1.0e-4 1000 10000 + reset_timestep 0 +# only output atoms near vacancy + #dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z -fix 1 all neb 1.0 +fix 1 all neb 1.0 -thermo 100 +thermo 100 # run NEB for 2000 steps or to force tolerance timestep 0.01 -min_style quickmin +min_style quickmin -neb 0.0 0.01 100 100 10 final final.sivac +neb 0.0 0.01 100 100 10 final final.sivac