forked from lijiext/lammps
119 lines
2.8 KiB
Plaintext
119 lines
2.8 KiB
Plaintext
# 3d EAM surface for local HD
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# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
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# hop event on (100) surface is same distance
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# exchange event is 2 atoms moving same distance
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variable Tequil index 400.0
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variable Vmax index 0.4
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variable qfactor index 0.3
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variable cutbond index 3.2
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variable Dcut index 10.0
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variable cutevent index 1.1
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variable alpha index 200.0
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variable boost index 4000.0
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variable ghostcut index 12.0
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variable steps index 1500
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variable nevent index 100
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variable nx index 8
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variable ny index 8
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variable zoom index 1.8
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variable seed index 826626413
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variable tol index 1.0e-15
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variable add index 37K
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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comm_modify cutoff ${ghostcut}
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lattice fcc 3.92
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region box block 0 6 0 6 0 4
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create_box 2 box
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create_atoms 1 box
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mass * 1.0
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change_box all z final -0.1 5.0 boundary p p f
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# replicate in xy
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replicate ${nx} ${ny} 1
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# add adatoms
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include adatoms.list.${add}
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# define frozen substrate and mobile atoms
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region base block INF INF INF INF 0 1.8
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set region base type 2
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group base type 2
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group mobile type 1
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# pair style
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pair_style eam/alloy
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pair_coeff * * ptvoterlammps.eam Pt Pt
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neighbor 0.5 bin
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neigh_modify every 1 delay 5 check yes
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fix 1 mobile nve
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fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
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timestep 0.005
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compute tmobile mobile temp
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thermo 100
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thermo_modify temp tmobile
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# thermal equilibration
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run 1000
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reset_timestep 0
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# pin base so will not move during quenches
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fix freeze base setforce 0.0 0.0 0.0
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# event detection
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compute event all event/displace ${cutevent}
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# hyper/local
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fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} &
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${Dcut} ${alpha} ${boost}
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# thermo output
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thermo_style custom step temp pe f_HL f_HL[*]
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thermo_modify lost ignore
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thermo_modify temp tmobile
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thermo ${nevent}
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# dump
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region substrate block INF INF INF INF 1.8 3.8
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region adatoms block INF INF INF INF 3.8 INF
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variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
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dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
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zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
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dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
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# test of histogramming and dump output of bias coeffs
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#fix histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL &
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# mode vector kind local file tmp.histo
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#dump 2 all local 1000 tmp.local f_HL
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# run
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hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
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