#############################################
#	 	  Cross-Linking of Amorphous		#
#			   FIX BOND/REACT				#
#############################################

clear
echo screen


#################################################
#	 			INITIALIZATION					#
#################################################
 units real
 boundary p p p
 atom_style full
 pair_style lj/class2/coul/long 15.0
 pair_modify mix arithmetic
 bond_style class2
 angle_style class2
 improper_style class2
 dihedral_style class2
 kspace_style ewald 1e-06
 
 
#################################################
#	 			DATA FILES						#
#################################################
 read_data longrun3.data &
			extra/bond/per/atom 1 &
			extra/angle/per/atom 3 &
			extra/dihedral/per/atom 64 &
			extra/improper/per/atom 11 &
			extra/special/per/atom 25


#################################################
#	 			Cross-Linking					#
#################################################
 velocity all create 100.0 4928459 dist gaussian

 molecule mol1 unreacted_rxn6.data_template
 molecule mol2 reacted_rxn6.data_template
# molecule mol3 unreacted_rxn4.data_template
# molecule mol4 reacted_rxn4.data_template

 thermo 50

 dump 1 all xyz 100 test_vis.xyz

 fix myrxns all bond/react stabilization yes statted_grp 0.03 &
		react myrxn1 all 1 0 14.25 mol1 mol2 rxn6_map &
#		react myrxn2 all 1 0 3.25 mol3 mol4 rxn4_map &

# stable at 800K
 fix 1 statted_grp_REACT npt temp 100.0 100.0 100.0 iso 1.0 1.0 1000.0

# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
 fix 2 bond_react_MASTER_group temp/rescale 1 100.0 100.0 10 1

 thermo_style custom step temp press density f_myrxns[1] #f_myrxns[2]  #cumulative reaction counts

# restart 100 restart1 restart2

 run 5000

 write_restart longrun4.restart
 write_data longrun4.data