Commit d7a479d2 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

hyper example dir

parent 0c8ce199

examples/README

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@@ -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

examples/hyper/adatoms.list.37K

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examples/hyper/in.hyper.global

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# 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

examples/hyper/in.hyper.local

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# 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

examples/hyper/ptvoterlammps.eam

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