# It is recommended to look at the LAMMPS documnetation for each of the command :DC
# set periodic boundaries, units and thero-baro damping
boundary p p p
atom_style atomic 
units metal
variable THERMO_DAMP equal 0.1
variable BARO_DAMP equal 0.5

# reads the input file
read_data in.str

# declares the atomic masses for the elements
# mass 1 55.845 #Fe
# mass 2 58.693 #Ni
# mass 3 51.996 #Cr
# mass 4 58.933 #Co
# mass 5 63.546 #Cu


#declaring the groups for convenience
# group     Fe type 1 
# group     Ni type 2
# group     Cr type 3
# group     Co type 4
# group     Cu type 5 

#set the charge
 #set           group  Fe  charge +0.0
 #set           group  Ni  charge +0.0
 #set           group  Cr  charge +0.0
 #set           group  Co  charge +0.0
 #set          group  Cu  charge +0.0


#Declaring the type of potential
pair_style   eam/alloy 
pair_coeff * * CoCuFeNiPd.set Co Cu Fe Ni Pd #Giving the path of the potential file

#neighbor 1.0 bin
#neigh_modify delay 10 check yes 


#########################

#Initiates the MD
reset_timestep	0 
velocity all create 300 986418 #temp and seed

#Fixing the temperature pf the system at certain temperature and pressure

fix 1 all npt temp 300 300 0.1 iso 0 0 1
fix 3 all atom/swap 100 100 29494 300 ke no types 1 2
fix 4 all atom/swap 100 100 29494 300 ke no types 1 3
fix 5 all atom/swap 100 100 29494 300 ke no types 1 4
fix 6 all atom/swap 100 100 29494 300 ke no types 1 5
fix 7 all atom/swap 100 100 29494 300 ke no types 2 3
fix 8 all atom/swap 100 100 29494 300 ke no types 2 4
fix 9 all atom/swap 100 100 29494 300 ke no types 2 5
fix 10 all atom/swap 100 100 29494 300 ke no types 3 4
fix 11 all atom/swap 100 100 29494 300 ke no types 3 5
fix 12 all atom/swap 100 100 29494 300 ke no types 4 5

#List the molecular configurations after every 25000 steps (10 images during the simulation)
dump  all_atoms3  all xyz 10000 pos-md-*.dump
dump_modify all_atoms3 element Co Cu Fe Ni Pd


#Timestep (in ps units) 
timestep     0.0005

#run the dynamics upto this number of steps (timestep * runtime / 1000 = total time in ns; 5ns right now)
run 100000


##############################