mirror of https://github.com/lammps/lammps.git
hyper example dir
This commit is contained in:
Steve Plimpton
parent
0c8ce199af
commit
d7a479d2f6
|
|
@ -78,6 +78,7 @@ friction: frictional contact of spherical asperities between 2d surfaces
|
|||
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
|
||||
granregion: use of fix wall/region/gran as boundary on granular particles
|
||||
hugoniostat: Hugoniostat shock dynamics
|
||||
hyper: global and local hyperdynamics of diffusion on Pt surface
|
||||
indent: spherical indenter into a 2d solid
|
||||
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
||||
latte: use of LATTE density-functional tight-binding quantum code
|
||||
|
|
|
|||
|
|
@ -0,0 +1,184 @@
|
|||
create_atoms 1 single 27.5 9.5 4
|
||||
create_atoms 1 single 16 9 4
|
||||
create_atoms 1 single 10 12 4
|
||||
create_atoms 1 single 31 44 4
|
||||
create_atoms 1 single 13 17 4
|
||||
create_atoms 1 single 8.5 28.5 4
|
||||
create_atoms 1 single 23 26 4
|
||||
create_atoms 1 single 38 27 4
|
||||
create_atoms 1 single 37.5 4.5 4
|
||||
create_atoms 1 single 41.5 47.5 4
|
||||
create_atoms 1 single 20.5 37.5 4
|
||||
create_atoms 1 single 5 8 4
|
||||
create_atoms 1 single 2.5 16.5 4
|
||||
create_atoms 1 single 38.5 45.5 4
|
||||
create_atoms 1 single 9 0 4
|
||||
create_atoms 1 single 39 32 4
|
||||
create_atoms 1 single 45.5 11.5 4
|
||||
create_atoms 1 single 40 0 4
|
||||
create_atoms 1 single 44.5 2.5 4
|
||||
create_atoms 1 single 4.5 44.5 4
|
||||
create_atoms 1 single 24.5 13.5 4
|
||||
create_atoms 1 single 47.5 23.5 4
|
||||
create_atoms 1 single 1 20 4
|
||||
create_atoms 1 single 38.5 31.5 4
|
||||
create_atoms 1 single 12.5 12.5 4
|
||||
create_atoms 1 single 2 27 4
|
||||
create_atoms 1 single 21 5 4
|
||||
create_atoms 1 single 47 12 4
|
||||
create_atoms 1 single 32.5 46.5 4
|
||||
create_atoms 1 single 9.5 40.5 4
|
||||
create_atoms 1 single 8.5 2.5 4
|
||||
create_atoms 1 single 41.5 22.5 4
|
||||
create_atoms 1 single 29 11 4
|
||||
create_atoms 1 single 3.5 3.5 4
|
||||
create_atoms 1 single 5 21 4
|
||||
create_atoms 1 single 46.5 31.5 4
|
||||
create_atoms 1 single 35 46 4
|
||||
create_atoms 1 single 40.5 41.5 4
|
||||
create_atoms 1 single 10 22 4
|
||||
create_atoms 1 single 43.5 14.5 4
|
||||
create_atoms 1 single 42 42 4
|
||||
create_atoms 1 single 4 26 4
|
||||
create_atoms 1 single 19 34 4
|
||||
create_atoms 1 single 33 9 4
|
||||
create_atoms 1 single 0.5 45.5 4
|
||||
create_atoms 1 single 30.5 32.5 4
|
||||
create_atoms 1 single 25.5 5.5 4
|
||||
create_atoms 1 single 47.5 39.5 4
|
||||
create_atoms 1 single 15 13 4
|
||||
create_atoms 1 single 21 21 4
|
||||
create_atoms 1 single 14 28 4
|
||||
create_atoms 1 single 9 34 4
|
||||
create_atoms 1 single 7 38 4
|
||||
create_atoms 1 single 11 35 4
|
||||
create_atoms 1 single 20.5 45.5 4
|
||||
create_atoms 1 single 30.5 31.5 4
|
||||
create_atoms 1 single 32.5 2.5 4
|
||||
create_atoms 1 single 21.5 3.5 4
|
||||
create_atoms 1 single 23 12 4
|
||||
create_atoms 1 single 4.5 33.5 4
|
||||
create_atoms 1 single 46 43 4
|
||||
create_atoms 1 single 42.5 45.5 4
|
||||
create_atoms 1 single 4.5 10.5 4
|
||||
create_atoms 1 single 33.5 15.5 4
|
||||
create_atoms 1 single 24 5 4
|
||||
create_atoms 1 single 13 16 4
|
||||
create_atoms 1 single 16.5 23.5 4
|
||||
create_atoms 1 single 45.5 28.5 4
|
||||
create_atoms 1 single 44.5 5.5 4
|
||||
create_atoms 1 single 27.5 46.5 4
|
||||
create_atoms 1 single 44.5 12.5 4
|
||||
create_atoms 1 single 12 41 4
|
||||
create_atoms 1 single 6 4 4
|
||||
create_atoms 1 single 31.5 10.5 4
|
||||
create_atoms 1 single 1 44 4
|
||||
create_atoms 1 single 31 4 4
|
||||
create_atoms 1 single 21 33 4
|
||||
create_atoms 1 single 3 33 4
|
||||
create_atoms 1 single 15 10 4
|
||||
create_atoms 1 single 28.5 22.5 4
|
||||
create_atoms 1 single 43 1 4
|
||||
create_atoms 1 single 3.5 0.5 4
|
||||
create_atoms 1 single 41 37 4
|
||||
create_atoms 1 single 18.5 43.5 4
|
||||
create_atoms 1 single 17 27 4
|
||||
create_atoms 1 single 3 5 4
|
||||
create_atoms 1 single 18.5 23.5 4
|
||||
create_atoms 1 single 31.5 14.5 4
|
||||
create_atoms 1 single 41 31 4
|
||||
create_atoms 1 single 22 3 4
|
||||
create_atoms 1 single 14.5 40.5 4
|
||||
create_atoms 1 single 9 38 4
|
||||
create_atoms 1 single 36 42 4
|
||||
create_atoms 1 single 33 22 4
|
||||
create_atoms 1 single 15.5 47.5 4
|
||||
create_atoms 1 single 3 0 4
|
||||
create_atoms 1 single 25.5 27.5 4
|
||||
create_atoms 1 single 2.5 28.5 4
|
||||
create_atoms 1 single 29.5 28.5 4
|
||||
create_atoms 1 single 44.5 18.5 4
|
||||
create_atoms 1 single 26 40 4
|
||||
create_atoms 1 single 41 27 4
|
||||
create_atoms 1 single 39.5 5.5 4
|
||||
create_atoms 1 single 3 38 4
|
||||
create_atoms 1 single 35 29 4
|
||||
create_atoms 1 single 11 19 4
|
||||
create_atoms 1 single 18 1 4
|
||||
create_atoms 1 single 39.5 40.5 4
|
||||
create_atoms 1 single 46 17 4
|
||||
create_atoms 1 single 1.5 23.5 4
|
||||
create_atoms 1 single 28.5 23.5 4
|
||||
create_atoms 1 single 10 28 4
|
||||
create_atoms 1 single 19 47 4
|
||||
create_atoms 1 single 10.5 16.5 4
|
||||
create_atoms 1 single 38 45 4
|
||||
create_atoms 1 single 42.5 41.5 4
|
||||
create_atoms 1 single 47.5 42.5 4
|
||||
create_atoms 1 single 38 7 4
|
||||
create_atoms 1 single 10 44 4
|
||||
create_atoms 1 single 29.5 27.5 4
|
||||
create_atoms 1 single 45 30 4
|
||||
create_atoms 1 single 3 9 4
|
||||
create_atoms 1 single 8.5 35.5 4
|
||||
create_atoms 1 single 24 44 4
|
||||
create_atoms 1 single 47 4 4
|
||||
create_atoms 1 single 7.5 8.5 4
|
||||
create_atoms 1 single 32.5 41.5 4
|
||||
create_atoms 1 single 0.5 34.5 4
|
||||
create_atoms 1 single 11 8 4
|
||||
create_atoms 1 single 2 40 4
|
||||
create_atoms 1 single 25 24 4
|
||||
create_atoms 1 single 47.5 6.5 4
|
||||
create_atoms 1 single 39.5 28.5 4
|
||||
create_atoms 1 single 17 21 4
|
||||
create_atoms 1 single 32 43 4
|
||||
create_atoms 1 single 16.5 29.5 4
|
||||
create_atoms 1 single 34 34 4
|
||||
create_atoms 1 single 11.5 3.5 4
|
||||
create_atoms 1 single 39 22 4
|
||||
create_atoms 1 single 24.5 36.5 4
|
||||
create_atoms 1 single 33 31 4
|
||||
create_atoms 1 single 35.5 35.5 4
|
||||
create_atoms 1 single 14.5 34.5 4
|
||||
create_atoms 1 single 34 28 4
|
||||
create_atoms 1 single 37 41 4
|
||||
create_atoms 1 single 33 46 4
|
||||
create_atoms 1 single 27.5 28.5 4
|
||||
create_atoms 1 single 40.5 22.5 4
|
||||
create_atoms 1 single 27.5 1.5 4
|
||||
create_atoms 1 single 12 2 4
|
||||
create_atoms 1 single 36 43 4
|
||||
create_atoms 1 single 28.5 9.5 4
|
||||
create_atoms 1 single 20.5 25.5 4
|
||||
create_atoms 1 single 3 3 4
|
||||
create_atoms 1 single 38 33 4
|
||||
create_atoms 1 single 3 20 4
|
||||
create_atoms 1 single 35 11 4
|
||||
create_atoms 1 single 5 25 4
|
||||
create_atoms 1 single 36.5 6.5 4
|
||||
create_atoms 1 single 19.5 24.5 4
|
||||
create_atoms 1 single 27 41 4
|
||||
create_atoms 1 single 39.5 11.5 4
|
||||
create_atoms 1 single 21.5 2.5 4
|
||||
create_atoms 1 single 46.5 15.5 4
|
||||
create_atoms 1 single 13 24 4
|
||||
create_atoms 1 single 11 37 4
|
||||
create_atoms 1 single 11.5 31.5 4
|
||||
create_atoms 1 single 47 0 4
|
||||
create_atoms 1 single 25.5 17.5 4
|
||||
create_atoms 1 single 32 11 4
|
||||
create_atoms 1 single 8 17 4
|
||||
create_atoms 1 single 27.5 12.5 4
|
||||
create_atoms 1 single 25 7 4
|
||||
create_atoms 1 single 25.5 37.5 4
|
||||
create_atoms 1 single 12 15 4
|
||||
create_atoms 1 single 1 7 4
|
||||
create_atoms 1 single 18.5 47.5 4
|
||||
create_atoms 1 single 5 38 4
|
||||
create_atoms 1 single 42 19 4
|
||||
create_atoms 1 single 30.5 7.5 4
|
||||
create_atoms 1 single 42.5 7.5 4
|
||||
create_atoms 1 single 26.5 18.5 4
|
||||
create_atoms 1 single 18.5 1.5 4
|
||||
create_atoms 1 single 41.5 10.5 4
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
# 3d EAM surface for global HD
|
||||
|
||||
# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
|
||||
# hop event on (100) surface is same distance
|
||||
# exchange event is 2 atoms moving same distance
|
||||
|
||||
variable Tequil index 800.0
|
||||
variable Vmax index 0.3
|
||||
variable qfactor index 0.3
|
||||
variable cutbond index 3.2
|
||||
variable cutevent index 1.1
|
||||
variable steps index 1000
|
||||
variable zoom index 1.8
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 3.92
|
||||
region box block 0 6 0 6 0 4
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 1.0
|
||||
|
||||
change_box all z final -0.1 5.0 boundary p p f
|
||||
create_atoms 2 single 3.5 3.5 4
|
||||
|
||||
# define frozen substrate and mobile atoms
|
||||
|
||||
group adatom type 2
|
||||
region base block INF INF INF INF 0 1.8
|
||||
set region base type 3
|
||||
group base type 3
|
||||
group mobile type 1 2
|
||||
|
||||
# pair style
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ptvoterlammps.eam Pt Pt Pt
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 mobile nve
|
||||
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 4879387 zero yes
|
||||
|
||||
timestep 0.005
|
||||
|
||||
compute tmobile mobile temp
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp tmobile
|
||||
|
||||
# thermal equilibration
|
||||
|
||||
run 1000
|
||||
reset_timestep 0
|
||||
|
||||
# pin base so will not move during quenches
|
||||
|
||||
fix freeze base setforce 0.0 0.0 0.0
|
||||
|
||||
# event detection
|
||||
|
||||
compute event all event/displace ${cutevent}
|
||||
|
||||
# hyper/global
|
||||
|
||||
fix HG mobile hyper/global ${cutbond} ${qfactor} ${Vmax} ${Tequil}
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp pe f_HG &
|
||||
f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] &
|
||||
f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11]
|
||||
|
||||
thermo_modify lost ignore
|
||||
thermo_modify temp tmobile
|
||||
|
||||
thermo 100
|
||||
|
||||
# dump output options
|
||||
|
||||
region substrate block INF INF INF INF 1.8 3.8
|
||||
region adatoms block INF INF INF INF 3.8 INF
|
||||
variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
|
||||
|
||||
dump 1 all custom 10000000 dump.* id type x y z
|
||||
dump_modify 1 pad 6
|
||||
|
||||
dump 5 all image 10000000 static.*.ppm v_acolor type &
|
||||
zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
|
||||
dump_modify 5 pad 9 amap 1 3 sa 1 3 blue red green
|
||||
|
||||
# run
|
||||
|
||||
hyper ${steps} 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5
|
||||
|
|
@ -0,0 +1,119 @@
|
|||
# 3d EAM surface for local HD
|
||||
|
||||
# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
|
||||
# hop event on (100) surface is same distance
|
||||
# exchange event is 2 atoms moving same distance
|
||||
|
||||
variable Tequil index 800.0
|
||||
variable Vmax index 0.3
|
||||
variable qfactor index 0.3
|
||||
variable cutbond index 3.2
|
||||
variable Dcut index 10.0
|
||||
variable cutevent index 1.1
|
||||
variable alpha index 200.0
|
||||
variable boost index 100.0
|
||||
variable ghostcut index 12.0
|
||||
variable steps index 1000
|
||||
variable nx index 1
|
||||
variable ny index 1
|
||||
variable zoom index 1.8
|
||||
variable seed index 59830932
|
||||
variable tol index 1.0e-15
|
||||
variable add index 184
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
comm_modify cutoff ${ghostcut}
|
||||
|
||||
lattice fcc 3.92
|
||||
region box block 0 6 0 6 0 4
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 1.0
|
||||
|
||||
change_box all z final -0.1 5.0 boundary p p f
|
||||
|
||||
# replicate in xy
|
||||
|
||||
replicate ${nx} ${ny} 1
|
||||
|
||||
# add adatoms
|
||||
|
||||
include adatoms.list.${add}
|
||||
|
||||
# define frozen substrate and mobile atoms
|
||||
|
||||
region base block INF INF INF INF 0 1.8
|
||||
set region base type 2
|
||||
group base type 2
|
||||
group mobile type 1
|
||||
|
||||
# pair style
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ptvoterlammps.eam Pt Pt
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 mobile nve
|
||||
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
|
||||
|
||||
timestep 0.005
|
||||
|
||||
compute tmobile mobile temp
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp tmobile
|
||||
|
||||
# thermal equilibration
|
||||
|
||||
run 1000
|
||||
reset_timestep 0
|
||||
|
||||
# pin base so will not move during quenches
|
||||
|
||||
fix freeze base setforce 0.0 0.0 0.0
|
||||
|
||||
# event detection
|
||||
|
||||
compute event all event/displace ${cutevent}
|
||||
|
||||
# hyper/local
|
||||
|
||||
fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} &
|
||||
${Dcut} ${alpha} ${boost}
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp pe f_HL &
|
||||
f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] &
|
||||
f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] &
|
||||
f_HL[14] f_HL[15] f_HL[16] f_HL[17]
|
||||
|
||||
thermo_modify lost ignore
|
||||
thermo_modify temp tmobile
|
||||
|
||||
thermo 100
|
||||
|
||||
# dump
|
||||
|
||||
write_dump all custom dump.initial id type x y z
|
||||
|
||||
variable Dhop equal 0.1
|
||||
variable check atom "c_dsp[4] > v_Dhop"
|
||||
compute dsp all displace/atom refresh check
|
||||
|
||||
dump 1 all custom 1000000000 dump.* id type x y z
|
||||
dump_modify 1 pad 6 thresh c_dsp[4] > ${Dhop} refresh c_dsp
|
||||
|
||||
dump 5 all image 10000000 static.*.ppm v_acolor type &
|
||||
zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
|
||||
dump_modify 5 pad 6 amap 1 3 sa 1 3 blue red green
|
||||
|
||||
# run
|
||||
|
||||
hyper ${steps} 100 HL event min ${tol} ${tol} 1000 1000 dump 1
|
||||
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue