# After running LAMMPS with this input script a number of dump files is created. 
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com


# ---------- Start simulation --------------------- 
clear
units metal 
dimension 3 
boundary f f f 
atom_style atomic 

# ========================== Create Atomistic Structure ===========================

region whole block 0 20 0 20 0 10
create_box 2 whole 

read_data 2particles.dat add append

region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2
group graphene1 type 1
group graphene2 type 2

pair_style hybrid/overlay lebedeva 20
pair_coeff * * none
pair_coeff 1 2 lebedeva CC.Lebedeva C C

mass 1 12.01 # Carbon
mass 2 12.01 # Carbon

neighbor 0.3 bin 
neigh_modify delay 1 check yes 

compute              peratom all pe/atom

dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3

thermo 10 
thermo_style custom step pe press temp
thermo_modify lost ignore

label STEP_LOOP

variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05

displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0

run 1

next MYSTEP
jump SELF STEP_LOOP

print "all done"