# 20 styrene molecules
# three reactions defined  

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2 

bond_style class2 

dihedral_style class2

improper_style class2

variable T equal 530

read_data tiny_polystyrene.data  &
  extra/bond/per/atom 5 &
  extra/angle/per/atom 15 &
  extra/dihedral/per/atom 15 &
  extra/improper/per/atom 25 &
  extra/special/per/atom 25

molecule mol1 2styrene_unreacted.data_template
molecule mol2 2styrene_reacted.data_template
molecule mol3 chain_plus_styrene_unreacted.data_template
molecule mol4 chain_plus_styrene_reacted.data_template
molecule mol5 chain_chain_unreacted.data_template
molecule mol6 chain_chain_reacted.data_template

thermo 100

# dump 1 all xyz 5 test_vis.xyz

fix rxn1 all bond/react stabilization yes statted_grp .03 &
 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 &
 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 &
 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100

fix 1 statted_grp_REACT nvt temp $T $T 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1

thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]

run 10000

# write_restart restart_longrun nofix
# write_data restart_longrun.data