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This commit is contained in:
Axel Kohlmeyer
2022-08-09 16:50:16 -04:00
parent 6eb51a68d9
commit 3a4a0078cd
4 changed files with 113 additions and 113 deletions
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70
examples/neb/in.neb.hop1
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@ -1,66 +1,66 @@
# 2d NEB surface simulation, hop from surface to become adatom # 2d NEB surface simulation, hop from surface to become adatom
dimension 2 dimension 2
boundary p s p boundary p s p
atom_style atomic atom_style atomic
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 5 neigh_modify delay 5
atom_modify map array sort 0 0.0 atom_modify map array sort 0 0.0
variable u uloop 20 variable u uloop 20
# create geometry with flat surface # create geometry with flat surface
lattice hex 0.9 lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25 region box block 0 20 0 10 -0.25 0.25
#create_box 3 box #create_box 3 box
#create_atoms 1 box #create_atoms 1 box
#mass * 1.0 #mass * 1.0
#write_data initial.hop1 #write_data initial.hop1
read_data initial.hop1 read_data initial.hop1
# LJ potentials # LJ potentials
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5 pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes pair_modify shift yes
# initial minimization to relax surface # initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000 minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0 reset_timestep 0
# define groups # define groups
region 1 block INF INF INF 1.25 INF INF region 1 block INF INF INF 1.25 INF INF
group lower region 1 group lower region 1
group mobile subtract all lower group mobile subtract all lower
set group lower type 2 set group lower type 2
timestep 0.05 timestep 0.05
# group of NEB atoms - either block or single atom ID 412 # group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box region surround block 10 18 17 20 0 0 units box
group nebatoms region surround group nebatoms region surround
#group nebatoms id 412 #group nebatoms id 412
set group nebatoms type 3 set group nebatoms type 3
group nonneb subtract all nebatoms group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0 fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d fix 3 all enforce2d
thermo 100 thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u #dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u #dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance # 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

60
examples/neb/in.neb.hop1.end
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@ -1,56 +1,56 @@
# 2d NEB surface simulation, hop from surface to become adatom # 2d NEB surface simulation, hop from surface to become adatom
dimension 2 dimension 2
boundary p s p boundary p s p
atom_style atomic atom_style atomic
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 5 neigh_modify delay 5
atom_modify map array sort 0 0.0 atom_modify map array sort 0 0.0
variable u uloop 20 variable u uloop 20
# create geometry with flat surface # create geometry with flat surface
lattice hex 0.9 lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25 region box block 0 20 0 10 -0.25 0.25
read_data initial.hop1.end read_data initial.hop1.end
# LJ potentials # LJ potentials
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5 pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes pair_modify shift yes
# define groups # define groups
region 1 block INF INF INF 1.25 INF INF region 1 block INF INF INF 1.25 INF INF
group lower region 1 group lower region 1
group mobile subtract all lower group mobile subtract all lower
set group lower type 2 set group lower type 2
timestep 0.05 timestep 0.05
# group of NEB atoms - either block or single atom ID 412 # group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box region surround block 10 18 17 20 0 0 units box
group nebatoms region surround group nebatoms region surround
#group nebatoms id 412 #group nebatoms id 412
set group nebatoms type 3 set group nebatoms type 3
group nonneb subtract all nebatoms group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0 fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0 fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d fix 3 all enforce2d
thermo 100 thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u #dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u #dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance # 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

74
examples/neb/in.neb.hop2
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@ -1,68 +1,68 @@
# 2d NEB surface simulation, hop of adatom on surface # 2d NEB surface simulation, hop of adatom on surface
dimension 2 dimension 2
boundary p s p boundary p s p
atom_style atomic atom_style atomic
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 5 neigh_modify delay 5
atom_modify map array sort 0 0.0 atom_modify map array sort 0 0.0
variable u uloop 20 variable u uloop 20
# create geometry with adatom # create geometry with adatom
lattice hex 0.9 lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25 region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25 region box1 block 0 20 0 10 -0.25 0.25
#create_box 3 box #create_box 3 box
#create_atoms 1 region box1 #create_atoms 1 region box1
#create_atoms 1 single 11.5 10.5 0 #create_atoms 1 single 11.5 10.5 0
#mass * 1.0 #mass * 1.0
#write_data initial.hop2 #write_data initial.hop2
read_data initial.hop2 read_data initial.hop2
# LJ potentials # LJ potentials
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5 pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes pair_modify shift yes
# initial minimization to relax surface # initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000 minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0 reset_timestep 0
# define groups # define groups
region 1 block INF INF INF 1.25 INF INF region 1 block INF INF INF 1.25 INF INF
group lower region 1 group lower region 1
group mobile subtract all lower group mobile subtract all lower
set group lower type 2 set group lower type 2
timestep 0.05 timestep 0.05
# group of NEB atoms - either block or single atom ID 421 # group of NEB atoms - either block or single atom ID 421
region surround block 10 18 17 21 0 0 units box region surround block 10 18 17 21 0 0 units box
group nebatoms region surround group nebatoms region surround
#group nebatoms id 421 #group nebatoms id 421
set group nebatoms type 3 set group nebatoms type 3
group nonneb subtract all nebatoms group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0 fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 fix 2 nebatoms neb 1.0
fix 3 all enforce2d fix 3 all enforce2d
thermo 100 thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u #dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u #dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance # 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

22
examples/neb/in.neb.sivac
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@ -5,7 +5,7 @@ units metal
atom_style atomic atom_style atomic
atom_modify map array atom_modify map array
boundary p p p boundary p p p
atom_modify sort 0 0.0 atom_modify sort 0 0.0
# coordination number cutoff # coordination number cutoff
@ -45,7 +45,7 @@ group Si type 1
group del id 300 group del id 300
delete_atoms group del compress no delete_atoms group del compress no
group vacneigh id 174 175 301 304 306 331 337 group vacneigh id 174 175 301 304 306 331 337
# choose potential # choose potential
pair_style sw pair_style sw
@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si
# set up neb run # set up neb run
variable u uloop 20 variable u uloop 20
# only output atoms near vacancy
# initial minimization to relax vacancy # initial minimization to relax vacancy
displace_atoms all random 0.1 0.1 0.1 123456 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 reset_timestep 0
# only output atoms near vacancy
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z #dump events vacneigh custom 1000 dump.neb.sivac.$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 # run NEB for 2000 steps or to force tolerance
timestep 0.01 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