#input file for machining
dimension  3                                     
boundary   s s p                                    
units metal    
atom_style  atomic
neighbor   2.0 bin
neigh_modify  delay 5
timestep    0.002

region     boundary1    block 0 1.95 0 36 0 36 units box
region     boundary2    block 1.95 36 0 1.95 0 36 units box
region     boundary     union  2  boundary1  boundary2
region     temp_layer1    block 1.95 3.95 1.95 36 0 36 units box
region     temp_layer2    block 3.95 36 1.95 3.95 0 36 units box
region     temp_layer     union  2  temp_layer1  temp_layer2
region     newton_layer  block 3.95 36 3.95 36 0 36 units box
region     piece union 3 boundary temp_layer newton_layer

create_box 2 piece

read_data      cube.dat add merge

pair_style      eam/fs
pair_coeff      * * Cu-Zr_4.eam.fs Cu Zr

group      boundary region boundary
group      temp_layer region temp_layer
group      newton_layer region newton_layer
group      mobile union temp_layer newton_layer

fix      01 boundary setforce 0.0 0.0 0.0

dump                1 all atom 100 step1.txt
thermo              1000
min_style           cg
minimize            1e-15 1e-15 5000 5000
undump              1
reset_timestep        0

velocity            temp_layer create 293 8877423

fix                  1 temp_layer nvt temp 293 293 1
thermo              1000
thermo_style     custom step temp etotal ke pe press pxx pyy pzz
dump              1 all atom 3000 step2.txt
run                 30000
undump              1
unfix               1

fix                 1 newton_layer nvt temp 293 293 1
thermo              1000
thermo_style     custom step temp etotal ke pe press pxx pyy pzz
dump                1 all atom 3000 step3.txt
run                 30000
undump         1
unfix               1

compute        new_temp temp_layer temp/com
thermo              1000
thermo_style     custom step temp etotal ke pe press pxx pyy pzz

dump                 1 all custom 1000 cut4.txt id type x y z vx vy vz fx fy fz

fix          20 newton_layer nve
fix          30 temp_layer nve
fix          31 temp_layer temp/rescale 10 293.0 293.0 10.0 1.0
fix_modify   31 temp new_temp
fix          40 boundary nve/noforce
run          100000