# 3d Lennard-Jones units lj atom_style molecular boundary p p p read_data test.data bond_style harmonic bond_coeff 1 10 1.1225 pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 2.5 velocity all create 1 87287 neighbor 1 bin fix 1 all nvt temp 1 1 0.1 dump mydump1 all atom 200 equiblium.lammpstrj thermo 10 minimize 1.0e-4 1.0e-6 100 1000 run 20000 undump mydump1 minimize 1.0e-4 1.0e-6 100 1000 reset_timestep 0 special_bonds lj 0 1 1 extra 2 fix cratebond all bond/create 200 1 2 1.0 1 iparam 2 3 jparam 1 4 prob 0.3679 19890202 dump mydump2 all atom 200 dumpreacte.lammpstrj compute 2 all bond/local dist eng dump 2 all local 200 dumpbond.txt index c_2[1] c_2[2] compute 1 all property/local btype batom1 batom2 dump 3 all local 200 dumptest.lammpstrj c_1[1] c_1[2] c_1[3] variable type1 atom type==1 variable type2 atom type==2 variable type3 atom type==3 variable type4 atom type==4 group n1 dynamic all var type1 group n2 dynamic all var type2 group n3 dynamic all var type3 group n4 dynamic all var type4 variable n1 equal count(n1) variable n2 equal count(n2) variable n3 equal count(n3) variable n4 equal count(n4) thermo_style custom step temp pe v_n1 v_n2 v_n3 v_n4 run 80000 #write_data L.data