add stabilized vs unstabilized examples

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,

# by using the internally-created 'bond_react_MASTER_group', like so:

fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

# two monomer nylon example

# reaction produces a condensed water molecule

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

read_data tiny_nylon.data

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template

molecule mol2 rxn1_stp1_reacted.data_template

molecule mol3 rxn1_stp2_unreacted.data_template

molecule mol4 rxn1_stp2_reacted.data_template

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization no &

  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &

  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map

fix 1 all nve/limit .03

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run 1000

# write_restart restart_longrun

# write_data restart_longrun.data