units           metal
atom_style      atomic
boundary        p p f                    
neighbor        2 bin
neigh_modify    every 1 delay 0
timestep        0.0001                     
read_data       gp.data                 
replicate       50 26 6             
change_box      all z delta -3 60         
#region          box1 block 57 66 53 61 28 42 units box
region box1 sphere 61.5 57 35 10 units box
group           sphere region box1
set             group sphere type 2        
region          bot block INF INF INF INF INF 7 units box
group           bot region bot
pair_style      airebo 3.0
pair_coeff      * * CH.airebo C C

mass            1 12.01
mass            2 12.01
fix             001 bot setforce 0 0 0
velocity        bot set 0 0 0
velocity        all create 300 9899

thermo_style    custom step elapsed atoms temp press ke pe etotal enthalpy vol density
thermo          100
thermo_modify   lost ignore flush yes

dump            1 all atom 10 dump4.xyz


variable        zlo equal zlo
variable        zhi equal zhi
variable        total_z equal ${zhi}-${zlo}

variable        top_z_low equal ${zhi}-5
region          top block INF INF INF INF ${top_z_low} ${zhi} units box
group           top region top

fix             nvt_relax all nvt temp 300 300 0.1
run             1000000
unfix           nvt_relax

fix             nve all nve

variable        gamma equal 0.1
variable        Ge equal 1.0e17
variable        Ke equal 100.0
variable        nzgrid equal floor(${total_z}/2.0)+1
#fix             ttm all ttm efix 2 nz ${nzgrid} grid z couple ${Ge} Ce_coeff ${gamma} Ke ${Ke} Trep 300.0

variable        F_flu equal 1.6e4
variable        tau equal 432e-15
variable        delta_z equal 10.0
variable        area equal 1.0                         
variable        E_total equal ${F_flu}*${area}
variable        P_total equal ${E_total}/${tau}
variable        V_heat equal ${area}*${delta_z}*1e-10
variable        P_vol equal ${P_total}/${V_heat}
variable        P_vol_ev equal ${P_vol}*6.2415e-24

variable        heat_z_low equal ${zhi}-${delta_z}
region          heat_region block INF INF INF INF ${heat_z_low} ${zhi} units box
#fix             heat all ttm heating region heat_region power ${P_vol_ev} units ev/ps/ang^3
dump            t all custom 10 dumpt.lammpstrj id type x y z
variable        t_off equal 0.432
fix            heat_10t sphere  heat at ${t_off} #The coupling parameters for `at` and `${t_off}` must be set separately.
run             500
unfix              heat_10t
fix            heat_20t sphere  heat at ${t_off}
run             432
unfix              heat_20t
fix            heat_30t sphere  heat at ${t_off}
run             568
unfix              heat_30t
fix            heat_40t sphere  heat at ${t_off}
run             2000000
unfix              heat_40t
thermo          10
compute         layer_temp all chunk/atom bin/1d z lower ${zlo} delta 3.355 units box
compute         temp_layer all temp/chunk layer_temp
compute         temp_all all temp
compute         msd all msd
fix             msd_out all ave/time 100 10 1000 c_msd[1] c_msd[2] c_msd[3] c_msd[4] file msd.dat
compute         rdf all rdf 100
fix             rdf_out all ave/time 500 2 1000 c_rdf[1] c_rdf[2] file rdf.dat
fix             temp_out all ave/time 10 10 100 c_temp_all file temp_global.dat
fix             temp_layer_out all ave/time 10 10 100 c_temp_layer[*] file temp_layers.dat
fix             Te_out all ave/time 10 10 100 f_ttm[1] f_ttm[2] file Te.dat
dump            2 all custom 10 dump.lammpstrj id type x y z