# Molecular dynamics NVT script with class2 ff for simulated polymerization
#
#input params:
# infile id1 id2 cut
#
# General
units            real
atom_style       full
dimension        3
newton           on
boundary         p p p

# Style
pair_style       lj/class2/coul/long 15.0
pair_modify      shift no mix sixthpower
kspace_style     ewald 1.0e-4
bond_style       class2
angle_style      class2
dihedral_style   class2
improper_style   harmonic
special_bonds    lj 0 0 1 coul 0 0 1 angle yes dihedral yes extra 24

# Atom Definition
read_data        ${infile}

# Settings
dielectric       1.0
neighbor         2.0 bin
neigh_modify     delay 0 every 1 check yes
timestep         1.0
run_style        verlet

#Groups
group		link1 	id ${id1}
group		link2	id ${id2}
group		both	union link1 link2

#iparam:	 c1 ->  c  # 3 ->  5
#jparam		 c1 ->  c  # 3 ->  5
#new bondtypes:  c-c = 9
#		                    Nevery  itype  jtype   cutoff   bondtype  
fix		1 both 	bond/create  1       6      3      ${cut}      9 & 
	        iparam  1 5 &
		jparam 1 5 &
                atype 5 atype 6 atype 7 & 
                itype 5 itype 20 itype 17 itype 18 & 

 
fix 		2 all 	nve/limit 0.0001
run		1
unfix		2
unfix 		1
# Restart file
write_data      data.lmps

#flagfile schreiben
# DONE