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new hyper examples

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Steve Plimpton
2018-10-12 13:26:40 -06:00
parent d7a479d2f6
commit 3b7ebbb8df
17 changed files with 2292 additions and 73 deletions
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examples/hyper/in.hyper.local
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@ -4,22 +4,23 @@
# 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 Tequil index 400.0
variable Vmax index 0.4
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 boost index 4000.0
variable ghostcut index 12.0
variable steps index 1000
variable nx index 1
variable ny index 1
variable steps index 1500
variable nevent index 100
variable nx index 8
variable ny index 8
variable zoom index 1.8
variable seed index 59830932
variable seed index 826626413
variable tol index 1.0e-15
variable add index 184
variable add index 37K
units metal
atom_style atomic
@ -89,31 +90,23 @@ fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} &
# 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_style custom step temp pe f_HL f_HL[*]
thermo_modify lost ignore
thermo_modify temp tmobile
thermo 100
thermo ${nevent}
# dump
write_dump all custom dump.initial id type x y z
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)
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 &
dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
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
dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
# run
hyper ${steps} 100 HL event min ${tol} ${tol} 1000 1000 dump 1
hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1