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#3d contact simulation
units        metal
dimension     3
boundary      p p s
atom_style    atomic
neighbor      3.0 bin
neigh_modify  delay 5
# create geometry
region box block 0 80 0 80 0 100 units box
create_box 3 box
mass   1 64
mass   2 12
#atom region
region boundary block INF INF INF INF INF 35 units box
region coating block INF INF INF INF 35 40 units box
region tool cone z 40 40 0 18 40 60 units box
lattice fcc 3.6149
create_atoms 1 region boundary units box
lattice diamond 3.57
create_atoms 2 region coating units box
lattice diamond 3.57
create_atoms 3 region tool units box
# Eam Potentials
pair_style eam
pair_coeff * * Ni_u3.eam
# define groups
group boundary region boundary
group mobile subtract all boundary
group tool region tool
set group boundary type 1
set group mobile type 2
#initial velocities
compute new mobile temp/partial 0 0 1
velocity mobile create 0.1 482748 temp new
velocity tool set 0 0 -5 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0 0 0
fix 3 mobile temp/rescale 100 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.01
thermo 100
thermo_modify temp new
dump 1 all atom 500 dump.yahen.lammpstrj
run 2000
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dimension 3
boundary  s s p
newton  on

units metal
atom_style atomic

neighbor 2.0 bin
neigh_modify delay 5

lattice fcc  3.52 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region  box1 block 0 30 0 15 -3.0 3.0  side in units lattice
region  1    sphere 15.0 20.0 0.0 2.0 side in units lattice
region  box2 block 0 30 15 22 -3.0 3.0 units lattice
region  box3 block 0 0.5 15 22 -3.0 3.0
region  box4 block 29.5 30 15 22 -3.0 3.0
region  box  union 5 box1 1 box2 box3 box4 units lattice

create_box   3  box

mass 1 58.71
mass 2 58.71
mass 3 12

region 2 block INF INF INF 0.5 INF INF units lattice
region 3 block INF 0.5  INF INF INF INF units lattice
region 4 block 29.5 INF INF INF INF INF units lattice

create_atoms 1 region box1 units lattice
create_atoms 2 region 2 units lattice
create_atoms 2 region 3 units lattice
create_atoms 2 region 4 units lattice

delete_atoms region box3
delete_atoms region box4

lattice none
lattice diamond 3.57 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

create_atoms 3  region 1 units lattice

pair_style eam  
pair_coeff * *  Ni_u3.eam

# define groups


group        sphere         region 1
group               lower          region 2
group        leftboundary  region 3
group        rightboundary   region 4

group       boundary union lower rightboundary leftboundary
group                mobile subtract all boundary

set         group mobile type 1
set              group lower type 2
set         group leftboundary type 2
set         group rightboundary  type 2
set         group sphere type 3

# initial velocities


compute        new mobile temp
velocity        mobile create 0.1E-4  482748 temp new

fix                1 all nve
fix                2 boundary  setforce 0.0 0.0 0.0
fix                3 all temp/rescale 100 0.1E-4 0.1E-4 0.1E-7 1.0

# run with indenter

timestep        0.001
variable    y equal "0.8*ylat - step*dt*1.6*ylat"

fix                4 sphere move variable NULL v_y NULL NULL NULL NULL

thermo                100
thermo_modify          temp new

compute stress mobile stress/atom pair
compute displ mobile displace/atom
compute centro mobile centro/atom fcc
compute pe mobile pe/atom

dump 1 all custom 100 dump.*.trajectory id type xs ys zs c_stress[1]  c_stress[2] c_stress[3] c_centro c_pe c_displ[1] c_displ[2] c_displ[3]  c_displ[4]

run                3000

# run without indenter

variable    dy equal "step*dt*1.6*ylat-20.0"

fix                6 sphere move variable NULL v_dy NULL NULL NULL NULL
run                1000
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region tool cone z 40 40 0 18 40 60 units box
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