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# Jake practice run
units real
boundary p p p
atom_style full
log testing_log
kspace_style pppm 1.0e-2 # actually, this appears required to make LAMMPS to check 1-3 neighbors
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 yes statted_grp .03 &
react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
fix 1 statted_grp nvt temp 300 300 100
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]
restart 100 restart1 restart2
run 10000
write_restart restart_longrun
write_data restart_longrun.data