# GLOBAL VARIABLES variable T equal 300.0 variable eqout equal 1 variable pout equal 1 variable nout equal 1 variable dt equal 0.020 variable tdamp equal 0.185 #################################################################### # INITIALIZATION units nano dimension 3 boundary p p p ##################################################################### # INTERACTION POTENTIAL atom_style molecular read_data Linear_Chain_Crosslinking.dat & extra/bond/per/atom 1 & extra/special/per/atom 25 molecule mol1 Linear_Chain_pre.template molecule mol2 Linear_Chain_post.template pair_style lj/cut 30 pair_modify shift yes pair_coeff * * 0.414195 8.0 30 bond_style harmonic bond_coeff 1 2125 8.0 bond_coeff 2 1.0 20.0 angle_style harmonic angle_coeff 1 3105 180.0 special_bonds lj 0.0 0.0 1.0 neighbor 5.0 bin neigh_modify delay 0 every 1 check yes comm_modify cutoff 30.0 vel yes ##################################################################### # SET EQUILIBRATION OUTPUT variable Step1 equal "step" variable Temp1 equal "temp" variable EK1 equal "ke" variable EP1 equal "pe" variable Etotal1 equal "etotal" variable Epair1 equal "epair" variable Ebond1 equal "ebond" variable Eangle1 equal "eangle" variable Vol1 equal "vol" variable Pxx equal "pxx" variable Pyy equal "pyy" variable Pzz equal "pzz" variable Density equal "density" variable Press equal "press" variable Lx equal "lx" variable Ly equal "ly" variable Lz equal "lz" variable XY equal "xy" ################################################################################################################################################################### fix equilibration all print ${eqout} "${Step1} ${Temp1} ${EK1} ${EP1} ${Etotal1} ${Epair1} ${Ebond1} ${Eangle1} ${Press} ${Vol1} ${Lx} ${Ly} ${Lz} ${XY} ${Pxx} ${Pyy} ${Pzz} ${Density}" file equilibration.txt screen no dump coordinate all custom/gz ${pout} dump.lammpstrj.gz id mol type x y z ############################################################################### # ENERGY MINIMIZATION min_style cg minimize 1.0e-8 1.0e-8 100 100 reset_timestep 0 #compute 1 all property/local btype batom1 batom2 #compute 2 all bond/local dist engpot force #dump bond_list all local 1 BondList.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] c_2[3] velocity all create ${T} 579632 #dist uniform units box fix 100 all bond/react react myrx all 1 17 23 mol1 mol2 Linear_Chain_map.txt prob 1.0 36978 fix 111 all ave/time 1 1 ${nout} f_100[1] file React.txt ################################################################################# # EQUILIBRATION (NVT dynamics at 300K) fix 1 all nvt temp 300 300 100 #fix 1 all nve #fix 2 all langevin ${T} ${T} ${tdamp} 32015 zero yes thermo 1 thermo_style custom step temp ke pe etotal epair ebond eangle lx ly lz xy vol pxx pyy pzz density f_100[1] timestep ${dt} run 1000