# LAMMPS Input File for stepped coating
# Programmed by Mai Trong Nghia, Aug. 14, 2013


# ---------- Initialize Simulation ------------------------------- 

clear 
units 		metal 
dimension 		3 
boundary        p s p
atom_style      atomic
variable latparam1 equal 3.615

# ---------- Create Atomistic Structure -------------------------- 

lattice         fcc ${latparam1} orient x -1 1 0 orient y 0 0 1 orient z 1 1 0
region          whole block  -10.4  10.6 -5.0  5.0 -0.4  0.6  

create_box      2 whole

# ---------- Define subtrate  ------------------------------------

lattice         fcc ${latparam1} orient x -1 1 0 orient y 0 0 1 orient z 1 1 0
region          sub block  -10.4  10.6 -5.0  0.0 -0.4  0.6   

create_atoms    1 region sub

region          lower block INF INF INF -4.0 INF INF 
group           boundary region lower


mass 1 63.55
mass 2 63.55



# ---------- Define indenter tip ---------------------------------

lattice         fcc ${latparam1} orient x -1 1 0 orient y 0 0 1 orient z 1 1 0
region          indent block  -10.4  10.6 2.0 5.0 -0.4  0.6 


create_atoms    2 region indent

# ---------- Define Interatomic Potential ------------------------ 

pair_style	hybrid eam lj/cut 
pair_coeff	* * eam Cu_u3.eam
pair_coeff	1 2 lj/cut 0.0042038 3.37 4.0

# ---------- Define region ---------------------------------------

group		sub type 1
group		subtrate subtract sub boundary
group		indenter type 2
group      mobile subtract all boundary indenter
group		exc union boundary indenter

neighbor        2.0 bin
neigh_modify    delay 5 exclude group exc exc

# ---------- Define Settings ------------------------------------- 

compute 1 indenter group/group sub

compute csym all centro/atom fcc

compute eng indenter pe/atom 
compute eatoms indenter reduce sum c_eng

compute disp indenter displace/atom
compute datoms indenter reduce sum c_disp[2]

# ---------- Run  Indentation  ------------------------------------ 

fix		12 mobile temp/rescale 1 1 1 0.1 1.0
fix		5 indenter nve/noforce
fix		10 mobile nve

timestep 0.005 # ps 
thermo 10 
thermo_modify	lost warn
thermo_style custom step temp pe c_eatoms c_datoms c_1[2] c_1 

dump 1 all xyz 1000 MD_v5a.xyz 

run 2000 # number of timestep

displace_atoms indenter move 0 -3.0 0 units box

velocity	indenter set 0 -0.1 0 sum yes units box # give the indenter velocity 0.1A/ps in the y direction

run		14000 # number of timestep

print "All done"